SMED30004317

Overview
NameSMED30004317
Smed IDSMED30004317
Length (bp)601
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30004317 (SMED30004317) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004317 (SMED30004317) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30004317 (SMED30004317) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004317 (SMED30004317) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30004317

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 35

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30004317h1SMcG0002123 Contig3771GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012030 Contig3640GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012029 Contig3771GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012029 Contig3640GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012028 Contig3771GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012028 Contig3640GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012030 Contig3771GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012034 Contig3640GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012034 Contig3771GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012033 Contig3640GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004317h1SMcG0012033 Contig3771GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004317h1SMcG0012028 Contig35762uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004317h1SMcG0012028 Contig35762newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
testisSMED30004317h1SMcG0002123 Contig3771GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30004317h1SMcG0012029 Contig3771GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30004317h1SMcG0012028 Contig3771GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30004317h1SMcG0012030 Contig3771GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30004317h1SMcG0012034 Contig3771GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30004317h1SMcG0012033 Contig3771GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
epidermisSMED30004317h1SMcG0012028 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30004317h1SMcG0012029 dd_Smed_v4_2300_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004317 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000387:65433..66033 -2978
Homology
[Close]
BLAST of SMED30004317 vs. Ensembl Human
Match: ABCA4 (ATP binding cassette subfamily A member 4 [Source:HGNC Symbol;Acc:HGNC:34])

HSP 1 Score: 47.7506 bits (112), Expect = 5.497e-6
Identity = 34/100 (34.00%), Postives = 53/100 (53.00%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLE-VKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLKSKFGD Y V + + S K  +   L  V+   + NF    S++ E    +L  F +S   L+ IF      K   LI +++V QT+LD++F++  K +
Sbjct:  948 HLKSKFGDGYIVTMKIKSPKDDLLPDLNPVEQFFQGNFPG--SVQRERHYNML-QFQVSSSSLARIFQLLLSHKDSLLIEEYSVTQTTLDQVFVNFAKQQ 1044
[Close]
BLAST of SMED30004317 vs. Ensembl Human
Match: ABCA4 (ATP binding cassette subfamily A member 4 [Source:HGNC Symbol;Acc:HGNC:34])

HSP 1 Score: 47.7506 bits (112), Expect = 6.241e-6
Identity = 34/100 (34.00%), Postives = 53/100 (53.00%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLE-VKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLKSKFGD Y V + + S K  +   L  V+   + NF    S++ E    +L  F +S   L+ IF      K   LI +++V QT+LD++F++  K +
Sbjct: 2156 HLKSKFGDGYIVTMKIKSPKDDLLPDLNPVEQFFQGNFPG--SVQRERHYNML-QFQVSSSSLARIFQLLLSHKDSLLIEEYSVTQTTLDQVFVNFAKQQ 2252
[Close]
BLAST of SMED30004317 vs. Ensembl Human
Match: ABCA12 (ATP binding cassette subfamily A member 12 [Source:HGNC Symbol;Acc:HGNC:14637])

HSP 1 Score: 47.7506 bits (112), Expect = 6.359e-6
Identity = 30/100 (30.00%), Postives = 54/100 (54.00%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLE-VKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            H+KS+FG  + VK+HL + K  +    + ++L   K +     +KD++   L Y   ++   +++IF      K    I +F V QT+L+E+FI+  KD+
Sbjct: 2157 HIKSRFGRGFTVKVHLKNNKVTMETLTKFMQLHFPKTY-----LKDQHLSMLEYHVPVTAGGVANIFDLLETNKTALNITNFLVSQTTLEEVFINFAKDQ 2251
[Close]
BLAST of SMED30004317 vs. Ensembl Human
Match: ABCA12 (ATP binding cassette subfamily A member 12 [Source:HGNC Symbol;Acc:HGNC:14637])

HSP 1 Score: 47.7506 bits (112), Expect = 6.400e-6
Identity = 30/100 (30.00%), Postives = 54/100 (54.00%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLE-VKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            H+KS+FG  + VK+HL + K  +    + ++L   K +     +KD++   L Y   ++   +++IF      K    I +F V QT+L+E+FI+  KD+
Sbjct: 2475 HIKSRFGRGFTVKVHLKNNKVTMETLTKFMQLHFPKTY-----LKDQHLSMLEYHVPVTAGGVANIFDLLETNKTALNITNFLVSQTTLEEVFINFAKDQ 2569
[Close]
BLAST of SMED30004317 vs. Ensembl Zebrafish
Match: abca1a (ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12])

HSP 1 Score: 51.2174 bits (121), Expect = 2.535e-7
Identity = 32/99 (32.32%), Postives = 51/99 (51.52%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK+KFGD Y + +    R      RLE  +   +    G ++K+++   L Y    S   L+ IF    K K    I D++V QT+LD++F++  KD+
Sbjct: 2137 HLKNKFGDGYTIIL----RVAGADPRLEPVMEFIERELPGSTLKEKHRNMLQYQLSSSLTSLARIFNILSKNKEQLHIEDYSVSQTTLDQVFVNFAKDQ 2231
[Close]
BLAST of SMED30004317 vs. Ensembl Zebrafish
Match: abca1a (ATP-binding cassette, sub-family A (ABC1), member 1A [Source:ZFIN;Acc:ZDB-GENE-031006-12])

HSP 1 Score: 51.2174 bits (121), Expect = 2.535e-7
Identity = 32/99 (32.32%), Postives = 51/99 (51.52%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK+KFGD Y + +    R      RLE  +   +    G ++K+++   L Y    S   L+ IF    K K    I D++V QT+LD++F++  KD+
Sbjct: 2137 HLKNKFGDGYTIIL----RVAGADPRLEPVMEFIERELPGSTLKEKHRNMLQYQLSSSLTSLARIFNILSKNKEQLHIEDYSVSQTTLDQVFVNFAKDQ 2231
[Close]
BLAST of SMED30004317 vs. Ensembl Mouse
Match: Abca12 (ATP-binding cassette, sub-family A (ABC1), member 12 [Source:MGI Symbol;Acc:MGI:2676312])

HSP 1 Score: 48.1358 bits (113), Expect = 3.203e-6
Identity = 30/100 (30.00%), Postives = 54/100 (54.00%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLE-VKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            H+KS+FG  + VK+HL + K  +    + ++L   K +     +KD++   L Y   ++   +++IF      K    I +F V QT+L+E+FI+  KD+
Sbjct: 2475 HIKSRFGRGFTVKVHLKNNKVSMETLTKFMQLHFPKTY-----LKDQHLSMLEYHVPVTAGGVANIFDLLETNKTALNITNFLVSQTTLEEVFINFAKDQ 2569
[Close]
BLAST of SMED30004317 vs. Ensembl Cavefish
Match: abca1a (ATP-binding cassette sub-family A member 1-like [Source:NCBI gene;Acc:103028164])

HSP 1 Score: 48.9062 bits (115), Expect = 1.351e-6
Identity = 30/99 (30.30%), Postives = 54/99 (54.55%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK++FGD Y + + +     Q    LE  +   ++   G ++K+++   L Y    S   L+ IF+   K K +  I D++V QT+LD++F++  KD+
Sbjct: 2139 HLKNRFGDGYTIVLRVAGADPQ----LEPVMKFIEHELPGSTLKEKHRNMLQYQLPSSLSSLARIFSILAKNKDELHIEDYSVSQTTLDQVFVNFAKDQ 2233
[Close]
BLAST of SMED30004317 vs. Ensembl Cavefish
Match: abca1a (ATP-binding cassette sub-family A member 1-like [Source:NCBI gene;Acc:103028164])

HSP 1 Score: 48.9062 bits (115), Expect = 1.351e-6
Identity = 30/99 (30.30%), Postives = 54/99 (54.55%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK++FGD Y + + +     Q    LE  +   ++   G ++K+++   L Y    S   L+ IF+   K K +  I D++V QT+LD++F++  KD+
Sbjct: 2139 HLKNRFGDGYTIVLRVAGADPQ----LEPVMKFIEHELPGSTLKEKHRNMLQYQLPSSLSSLARIFSILAKNKDELHIEDYSVSQTTLDQVFVNFAKDQ 2233
[Close]
BLAST of SMED30004317 vs. Ensembl Cavefish
Match: abca1a (ATP-binding cassette sub-family A member 1-like [Source:NCBI gene;Acc:103028164])

HSP 1 Score: 48.9062 bits (115), Expect = 1.538e-6
Identity = 30/99 (30.30%), Postives = 54/99 (54.55%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK++FGD Y + + +     Q    LE  +   ++   G ++K+++   L Y    S   L+ IF+   K K +  I D++V QT+LD++F++  KD+
Sbjct: 2092 HLKNRFGDGYTIVLRVAGADPQ----LEPVMKFIEHELPGSTLKEKHRNMLQYQLPSSLSSLARIFSILAKNKDELHIEDYSVSQTTLDQVFVNFAKDQ 2186
[Close]
BLAST of SMED30004317 vs. Ensembl Sea Lamprey
Match: abca12 (ATP-binding cassette, sub-family A (ABC1), member 12 [Source:ZFIN;Acc:ZDB-GENE-030131-9790])

HSP 1 Score: 47.7506 bits (112), Expect = 6.981e-7
Identity = 29/100 (29.00%), Postives = 56/100 (56.00%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDKV 300
            HLK++FG+ + +K+ L S   +++   EV   I  +F  G  +K+++   L +    +  KLS+IF    K K    I  +++ QT+LD++FI+  + ++
Sbjct: 1670 HLKNRFGNGHMIKLRLSSGNSKVT---EVTEFITSHF-PGAYLKEQHISQLEFQVPSNAGKLSEIFIALEKEKESLSIQHYSISQTTLDQVFINFARQQI 1765
[Close]
BLAST of SMED30004317 vs. Ensembl Medaka
Match: ENSORLT00000025407.2 (ATP-binding cassette sub-family A member 1 [Source:NCBI gene;Acc:101163308])

HSP 1 Score: 49.6766 bits (117), Expect = 7.680e-7
Identity = 32/99 (32.32%), Postives = 53/99 (53.54%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK++FGD Y + + +      +   L V   IE    SG ++K+++   L Y    S   L+ IF+   K K    I D++V QT+LD++F++  KD+
Sbjct: 2160 HLKNRFGDGYTIILRVAGPDPDL---LPVMKFIESEL-SGSTLKEKHRNMLQYQLPSSLTSLAHIFSILAKNKDTLRIEDYSVTQTTLDQVFVNFAKDQ 2254
[Close]
BLAST of SMED30004317 vs. Ensembl Medaka
Match: abca12 (ATP-binding cassette, sub-family A (ABC1), member 12 [Source:ZFIN;Acc:ZDB-GENE-030131-9790])

HSP 1 Score: 47.7506 bits (112), Expect = 3.567e-6
Identity = 32/111 (28.83%), Postives = 58/111 (52.25%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFID-CVKDKVLLTIPYENPE 330
            H+K++FG  + V+++L    C +     +   +++ F S   +KD++F  + Y    +   ++DIF      K    I  F+V QT+LDE+FI+  + +  L T P +N E
Sbjct: 1798 HIKNRFGSGFTVRMYLAEASCDVE---AITDFMQRKFPS-TYLKDQHFTMVEYHVPTAPGGVADIFNQLESNKNTLQIKHFSVSQTTLDEVFINFAMGNTDLETTPIQNEE 1904
[Close]
BLAST of SMED30004317 vs. Ensembl Medaka
Match: abca12 (ATP-binding cassette, sub-family A (ABC1), member 12 [Source:ZFIN;Acc:ZDB-GENE-030131-9790])

HSP 1 Score: 47.3654 bits (111), Expect = 3.945e-6
Identity = 32/111 (28.83%), Postives = 58/111 (52.25%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFID-CVKDKVLLTIPYENPE 330
            H+K++FG  + V+++L    C +     +   +++ F S   +KD++F  + Y    +   ++DIF      K    I  F+V QT+LDE+FI+  + +  L T P +N E
Sbjct: 1516 HIKNRFGSGFTVRMYLAEASCDVE---AITDFMQRKFPS-TYLKDQHFTMVEYHVPTAPGGVADIFNQLESNKNTLQIKHFSVSQTTLDEVFINFAMGNTDLETTPIQNEE 1622
[Close]
BLAST of SMED30004317 vs. Ensembl Medaka
Match: abca1a (ATP-binding cassette sub-family A member 1 [Source:NCBI gene;Acc:101163147])

HSP 1 Score: 46.9802 bits (110), Expect = 6.404e-6
Identity = 30/99 (30.30%), Postives = 52/99 (52.53%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK++FGD Y + + +      +     V   IE+    G ++K+++   L Y    S   L+ IF+   K K    I D++V QT+LD++F++  KD+
Sbjct: 2105 HLKNRFGDGYTIILRVAGPDPDLR---PVMGFIEREL-PGSTLKEKHRNMLQYQLPSSLTSLARIFSLLSKNKETLCIEDYSVSQTTLDQVFVNFAKDQ 2199
[Close]
BLAST of SMED30004317 vs. Ensembl Medaka
Match: abca1a (ATP-binding cassette sub-family A member 1 [Source:NCBI gene;Acc:101163147])

HSP 1 Score: 46.9802 bits (110), Expect = 6.528e-6
Identity = 30/99 (30.30%), Postives = 52/99 (52.53%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLK++FGD Y + + +      +     V   IE+    G ++K+++   L Y    S   L+ IF+   K K    I D++V QT+LD++F++  KD+
Sbjct: 2135 HLKNRFGDGYTIILRVAGPDPDLR---PVMGFIEREL-PGSTLKEKHRNMLQYQLPSSLTSLARIFSLLSKNKETLCIEDYSVSQTTLDQVFVNFAKDQ 2229
[Close]
BLAST of SMED30004317 vs. Planmine SMEST
Match: SMESG000029534.1 (SMESG000029534.1)

HSP 1 Score: 186.037 bits (471), Expect = 3.595e-54
Identity = 91/92 (98.91%), Postives = 91/92 (98.91%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIF 276
            HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIE NFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIF
Sbjct: 1978 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIENNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIF 2069
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BLAST of SMED30004317 vs. Planmine SMEST
Match: SMESG000068605.1 (SMESG000068605.1)

HSP 1 Score: 90.8929 bits (224), Expect = 3.930e-21
Identity = 48/99 (48.48%), Postives = 70/99 (70.71%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDK 297
            HLKSKFGD+Y+VKI +   +   +   ++K  ++  F  G+S+KDENF+TL Y F+ S +KLS IF FF  +K +G+I D++V QTSLDE+FI+  K+K
Sbjct: 1921 HLKSKFGDDYFVKIRMNFIE---NESDKIKAIMKTQFPQGVSLKDENFITLQYRFNCS-LKLSTIFHFFENLKANGVIADYSVSQTSLDEVFINFAKNK 2015
[Close]
BLAST of SMED30004317 vs. Planmine SMEST
Match: SMESG000029537.1 (SMESG000029537.1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.395e-18
Identity = 42/94 (44.68%), Postives = 67/94 (71.28%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFID 282
            HLKSKFGD+YYVKI L+S + + ++  +VK  I++ F S +S++DENF TL Y F  S I++  +F FF +MK    I+D+++ Q +L+++FI+
Sbjct: 1896 HLKSKFGDDYYVKIRLHSGEAETNNHEKVKKIIQEAFLSDVSLRDENFATLQYQF-CSKIRIFKLFEFFEQMKATKTILDYSISQMTLEDVFIN 1988
[Close]
BLAST of SMED30004317 vs. Planmine SMEST
Match: SMESG000032891.1 (SMESG000032891.1)

HSP 1 Score: 80.1073 bits (196), Expect = 2.509e-17
Identity = 45/98 (45.92%), Postives = 63/98 (64.29%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKD 294
            HLKSKFGD+YYV I +   K   +   +VK  IE  F S +S  D +F+TL Y F  S  KL+ IF FF  +K D +I+D++V QT+LD++FI+  +D
Sbjct: 1885 HLKSKFGDDYYVTIRMPFGKDHANDNGKVKAIIEDKFPSEVSFVDGSFVTLQYRF-ASSTKLAVIFDFFENLKKDSIILDYSVSQTTLDDVFINFARD 1981
[Close]
BLAST of SMED30004317 vs. Planmine SMEST
Match: SMESG000056983.1 (SMESG000056983.1)

HSP 1 Score: 79.7221 bits (195), Expect = 3.287e-17
Identity = 41/98 (41.84%), Postives = 64/98 (65.31%), Query Frame = 1 
Query:    1 HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLTLLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKD 294
            HLKSKFG +YYVKI L+  +  +S R E++  I K   S   +K+EN + + Y FD S +KLS+IF  F  ++ + ++ +++V Q SLDE+FI+  K+
Sbjct: 1956 HLKSKFGHDYYVKIRLHPNRNSLSDRNEIETIINKEIWSSARMKEENAVIIEYRFDSS-VKLSNIFRVFEDLRTNEMVKEYSVSQMSLDEVFINFAKN 2052
The following BLAST results are available for this feature:
BLAST of SMED30004317 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 4
Match NameE-valueIdentityDescription
ABCA45.497e-634.00ATP binding cassette subfamily A member 4 [Source:... [more]
ABCA46.241e-634.00ATP binding cassette subfamily A member 4 [Source:... [more]
ABCA126.359e-630.00ATP binding cassette subfamily A member 12 [Source... [more]
ABCA126.400e-630.00ATP binding cassette subfamily A member 12 [Source... [more]
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BLAST of SMED30004317 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
abca1a2.535e-732.32ATP-binding cassette, sub-family A (ABC1), member ... [more]
abca1a2.535e-732.32ATP-binding cassette, sub-family A (ABC1), member ... [more]
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BLAST of SMED30004317 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Abca123.203e-630.00ATP-binding cassette, sub-family A (ABC1), member ... [more]
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BLAST of SMED30004317 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 3
Match NameE-valueIdentityDescription
abca1a1.351e-630.30ATP-binding cassette sub-family A member 1-like [S... [more]
abca1a1.351e-630.30ATP-binding cassette sub-family A member 1-like [S... [more]
abca1a1.538e-630.30ATP-binding cassette sub-family A member 1-like [S... [more]
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BLAST of SMED30004317 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
abca126.981e-729.00ATP-binding cassette, sub-family A (ABC1), member ... [more]
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BLAST of SMED30004317 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30004317 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 5
Match NameE-valueIdentityDescription
ENSORLT00000025407.27.680e-732.32ATP-binding cassette sub-family A member 1 [Source... [more]
abca123.567e-628.83ATP-binding cassette, sub-family A (ABC1), member ... [more]
abca123.945e-628.83ATP-binding cassette, sub-family A (ABC1), member ... [more]
abca1a6.404e-630.30ATP-binding cassette sub-family A member 1 [Source... [more]
abca1a6.528e-630.30ATP-binding cassette sub-family A member 1 [Source... [more]
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BLAST of SMED30004317 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000029534.13.595e-5498.91SMESG000029534.1[more]
SMESG000068605.13.930e-2148.48SMESG000068605.1[more]
SMESG000029537.11.395e-1844.68SMESG000029537.1[more]
SMESG000032891.12.509e-1745.92SMESG000032891.1[more]
SMESG000056983.13.287e-1741.84SMESG000056983.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004317 ID=SMED30004317|Name=SMED30004317|organism=Schmidtea mediterranea sexual|type=transcript|length=601bp
CATTTGAAATCGAAATTCGGTGATAATTATTACGTCAAGATACACTTGTA
TTCGAGAAAATGCCAAATAAGTCATCGGTTAGAGGTGAAATTGGCGATTG
AAAAAAATTTCAGGAGCGGAATAAGTATCAAAGATGAAAACTTTCTGACC
CTTCTCTATACTTTCGATTTATCATTTATTAAATTATCTGATATTTTTAC
TTTTTTTCATAAGATGAAAGTTGATGGTTTAATTATTGATTTTACCGTCT
ATCAAACTTCATTAGATGAAATTTTTATTGACTGTGTTAAAGATAAAGTG
CTCCTTACAATTCCTTATGAAAATCCGGAATTTACTCTCTCACCTCTCAC
AGAAAATGATATTGTTTGTTCCTTTGAAGAATCTCAAGGTCAAGTGACTT
TTGCTTAAGTTTTTTTGCCGTAGAATTTTCACTTTAAATTTTCTTATTAA
CAGTTGCTATTTTTGATTGTTTATCACTTTATATTTATCATGTGTTTTAA
TTCACTTATCCGACAAGTAATTATTCCCATGAGTTTTCTTTAACGAAATA
AAACAAATCTTTTTATTTTATTGTTACAATCTGCTTCATGTGTTTCTTTC
A
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protein sequence of SMED30004317-orf-1

>SMED30004317-orf-1 ID=SMED30004317-orf-1|Name=SMED30004317-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
HLKSKFGDNYYVKIHLYSRKCQISHRLEVKLAIEKNFRSGISIKDENFLT
LLYTFDLSFIKLSDIFTFFHKMKVDGLIIDFTVYQTSLDEIFIDCVKDKV
LLTIPYENPEFTLSPLTENDIVCSFEESQGQVTFA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell