SMED30013626

Overview
NameSMED30013626
Smed IDSMED30013626
Length (bp)411
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30013626 (SMED30013626) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013626 (SMED30013626) in cells (dots) of each of the 12 neoblast clusters.

 

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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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Alignments
SMED30013626 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007937:37220..37676 -1992
v31.035246:221..677 +1991
v31.004765:46260..46717 +1991
v31.036881:994..1450 +1982
v31.033292:3205..3661 +1982
v31.035502:3318..3778 -1977
v31.039770:1708..2166 -1975
v31.029808:5900..6354 -1975
v31.011596:16749..17201 -1975
v31.030317:1991..2446 -1974
v31.003451:40274..40729 +1974
v31.001977:1008..1472 -1973
v31.027160:5005..5465 +1967
v31.002579:60227..61539 +1965
v31.045459:480..936 -1962
v31.030758:1429..1891 -1960
v31.030769:2128..2585 +1959
v31.041292:2042..2499 +1958
v31.041907:1525..1977 -1957
v31.009462:854..1308 -1956
v31.043798:1374..1828 -1947
v31.029196:7780..8243 +1947
v31.000146:228723..229186 +1947
v31.000131:401..853 -1939
v31.029230:4380..4830 +1938
v31.049374:1850..2317 -1935
v31.007326:30073..30524 +1932
v31.031566:1561..2024 -1929
v31.024943:3206..3673 -1926
v31.036796:2590..3054 +1924
v31.032867:3068..3532 +1922
v31.000110:1607..2067 -1921
v31.001780:49130..49592 +1920
v31.027461:3884..4342 +1906
v31.016334:3839..4307 -1906
v31.000234:101106..101561 -1906
v31.039809:719..1176 +1905
v31.020828:1131..1577 +1905
v31.001204:70014..70471 -1903
v31.031857:3389..3848 +1894
v31.002634:50398..50849 -1894
v31.008072:1242..1686 -1888
v31.014450:18824..19284 -1886
v31.005584:29389..29846 -1885
v31.040662:1646..2099 +1883
v31.001147:23802..24263 -1881
v31.002960:88528..88986 +1876
v31.003181:47660..48117 -1870
v31.010689:22806..23265 +1869
v31.007032:18486..18936 +1867
v31.041781:4123..4562 -1862
v31.004799:24258..24714 +1862
v31.003882:68128..68588 -1857
v31.003260:5995..6452 +1850
v31.020290:290..747 -1844
v31.003893:3081..3532 -1843
v31.007740:13211..13668 -1840
v31.035763:1907..2333 -1839
v31.008947:33923..34380 -1837
v31.000816:98355..98842 -1837
v31.003859:37352..37807 +1836
v31.000893:103641..104096 -1835
v31.045634:1649..2106 +1832
v31.000559:24823..25280 -1832
v31.003844:37224..37681 -1831
v31.003189:42875..43332 +1831
v31.000237:167934..168387 +1831
v31.000328:73260..73715 +1828
v31.029377:3100..3555 -1827
v31.001255:24256..24711 +1827
v31.029460:701..1144 +1824
v31.018238:13195..13651 -1824
v31.013000:1838..2744 +1824
v31.000670:26216..26670 +1824
v31.012697:12768..13223 +1818
v31.010150:1676..2132 -1817
v31.000151:7565..8025 +1816
v31.000057:124197..124654 +1814
v31.002501:3407..3862 -1809
v31.000623:286..742 -1808
v31.020771:5142..5598 -1804
v31.003799:39595..40356 +1799
v31.021537:5429..5894 +1791
v31.001699:24080..24536 -1789
v31.010429:1360..1808 +1787
v31.005234:46959..47416 -1787
v31.000164:136344..136777 +1785
v31.013481:17485..17950 -1783
v31.035640:2890..3337 +1781
v31.028255:1489..1939 -1779
v31.009184:1248..1694 -1779
v31.000006:92395..92929 +1774
v31.014919:1645..2115 +1765
v31.006098:2076..2523 -1763
v31.003693:66478..66925 -1763
v31.022329:6896..7342 +1762
v31.002523:11648..12176 +1759
v31.000225:8747..9187 +1756
v31.000634:62822..63269 -1753
v31.000352:56351..56798 +1752
v31.006578:22223..22670 +1751
v31.025387:3710..4154 -1746
v31.004115:57833..58280 -1745
v31.047726:1649..2075 -1743
v31.024810:4543..4990 +1742
v31.016646:10251..10699 -1742
v31.001528:18480..18928 +1741
v31.000570:142711..143158 -1736
v31.000547:147015..147458 +1734
v31.000018:175607..176057 -1734
v31.015411:5560..6015 -1732
v31.009483:5476..5931 -1730
v31.013852:14598..15035 +1728
v31.004474:40051..40506 -1728
v31.003903:35008..35481 -1728
v31.006302:5753..6207 +1727
v31.003875:31944..32384 +1727
v31.003467:33343..33782 +1723
v31.010184:9458..9904 -1716
v31.000606:40494..40943 -1716
v31.000018:127063..127513 +1707
v31.008607:1587..2034 -1701
v31.007415:28393..28840 +1701
v31.002976:74335..74782 +1697
v31.007382:805..1251 -1696
v31.004151:38306..38764 -1696
v31.001681:1370..1816 -1696
v31.000227:92261..92707 -1696
v31.000473:170722..171161 +1693
v31.001966:1263..1703 +1692
v31.000302:83983..84490 -1692
v31.026459:486..932 -1691
v31.005817:10865..11309 +1691
v31.004844:49298..49741 +1690
v31.011885:4312..4759 +1688
v31.001162:71943..72387 +1687
v31.001019:15183..15627 +1687
v31.007643:13240..13686 +1682
v31.002609:35034..35476 -1680
v31.001595:31544..31994 +1672
v31.002649:82491..82937 +1669
v31.000735:44127..44563 +1666
v31.006992:10834..11281 +1665
v31.018697:97..551 +1663
v31.003473:990..1456 +1661
v31.006826:8100..8550 -1658
v31.000139:180080..180523 +1655
v31.025838:1090..1544 -1654
v31.000863:26230..26664 +1654
v31.001442:1430..1885 +1653
v31.007418:13114..13554 +1649
v31.005272:6850..7292 +1647
v31.001245:1433..1859 +1647
v31.019548:12914..13356 +1645
v31.024145:9995..12169 +1643
v31.009363:21568..22011 -1643
v31.004136:49448..49898 -1643
v31.018981:2734..3178 +1640
v31.005431:288..734 +1640
v31.001441:9794..10235 +1638
v31.016088:8250..8694 -1637
v31.000486:100931..101380 +1636
v31.012944:16291..16733 -1630
v31.017092:10710..11154 +1629
v31.017939:8648..9093 +1628
v31.013023:12560..13004 -1624
v31.003112:35023..35477 -1622
v31.011902:19127..19564 -1617
v31.002660:94270..94688 -1615
v31.011601:9153..9595 -1614
v31.000389:112946..113388 -1614
v31.032593:2295..2840 +1613
v31.023032:1570..2021 -1613
v31.007257:10838..11281 +1608
v31.011344:11124..11616 +1606
v31.008453:18775..19201 -1606
v31.021298:8818..9269 +1604
v31.017968:16074..16526 +1601
v31.013500:615..1058 -1600
v31.007197:13239..13686 +1600
v31.006396:16342..16781 -1600
v31.017448:8027..8474 +1599
v31.025562:3646..4096 +1594
v31.019298:566..1008 -1591
v31.005189:23405..23848 +1591
v31.012793:4395..4823 -1587
v31.010129:18588..19039 +1585
v31.002365:2718..3155 -1583
v31.011678:14413..14866 +1582
v31.001692:50566..51020 -1581
v31.000392:90639..91088 +1581
v31.004332:13430..13882 +1580
v31.017176:5085..5503 +1579
v31.014233:11044..11479 +1575
v31.003012:61061..61506 +1575
v31.015979:11785..12223 +1572
v31.013645:13828..14271 -1570
v31.026522:1663..2099 -1568
v31.002795:29853..30295 +1568
v31.035178:402..839 +1562
v31.011598:14746..15193 -1561
v31.002008:6526..6953 -1556
v31.015806:18156..18578 +1553
v31.008777:1..419 -1552
v31.003631:15798..16229 -1548
v31.033583:1806..2199 +1541
v31.018530:5802..6240 +1536
v31.025768:3790..4225 -1534
v31.010862:19919..20344 -1533
v31.011182:7035..7486 -1532
v31.012744:9773..10209 -1528
v31.019209:1174..1635 -1527
v31.008854:26357..26799 -1521
v31.003351:40709..41144 -1520
v31.030725:779..1222 -1517
v31.020608:6247..6704 -1517
v31.000479:164674..165119 +1505
v31.010651:3765..4145 -1504
v31.015796:690..1175 +1499
v31.009201:20441..20821 +1494
v31.008020:9804..10241 +1492
v31.012694:22616..23056 -1489
v31.019311:12187..12652 +1483
v31.044043:781..1157 -1482
v31.003687:28355..28786 +1480
v31.014718:3310..3742 -1471
v31.003683:46571..47007 -1464
v31.007258:27357..27798 -1450
v31.003112:5344..5782 -1446
v31.016606:2613..3004 +1439
v31.000733:113301..113747 +1427
v31.009017:20523..20939 -1418
v31.015900:6919..7316 -1414
v31.023715:2298..2714 -1400
v31.017951:2245..2677 +1393
v31.013420:6981..7396 +1383
v31.001553:37077..37496 -1374
v31.017356:8378..8800 +1353
v31.000296:107083..107516 +1331
v31.017099:5276..5733 +1321
v31.001156:36913..37313 -1300
v31.029571:987..1437 -1228
v31.003869:52468..52889 -1184
v31.022608:8048..8465 +1183
v31.010016:23747..24274 -1118
v31.027453:7452..7816 +1113
v31.030688:6986..7350 +1104
v31.013806:4929..5296 +1066
v31.008648:1096..1620 -1039
v31.027545:6662..7038 -1010
v31.000871:39728..40162 +973
v31.000719:15034..15550 -920
v31.001452:33439..33808 -898
v31.008648:1269..1674 -574
v31.024145:9328..9740 +509
Homology
BLAST of SMED30013626 vs. Planmine SMEST
Match: SMESG000055962.1 (SMESG000055962.1)

HSP 1 Score: 102.834 bits (255), Expect = 1.000e-27
Identity = 59/80 (73.75%), Postives = 59/80 (73.75%), Query Frame = 1
Query:   22 MAGQNNILRSLLTSSIGNFYLLFITINLLVNLDWFDVTENEDLLDLDDVFDCNNNNVERIIIEDTPTSINEDVYEVISIG 261
            MAGQ N LRS LTSSI             V  DWFDVTENEDLL LDDVFD NNNNVERIIIEDTPTSINEDVYEVI IG
Sbjct:    1 MAGQINYLRSRLTSSI-------------VYFDWFDVTENEDLLYLDDVFDRNNNNVERIIIEDTPTSINEDVYEVIFIG 67          
BLAST of SMED30013626 vs. Planmine SMEST
Match: SMESG000017989.1 (SMESG000017989.1)

HSP 1 Score: 82.0333 bits (201), Expect = 2.130e-21
Identity = 51/67 (76.12%), Postives = 56/67 (83.58%), Query Frame = 1
Query:   64 SIGNFY--LLFITINLLVNLDWFDVTENEDLLDLDDVFDCNNNNVERIIIEDTPTSINEDVYEVISI 258
             +G +Y  L+   +  +VN DWFDVTENEDLLDLDDVFDCNNNNVERIIIEDT TSINEDVYEVISI
Sbjct:  762 PMGFYYPALMVSKLQTMVNFDWFDVTENEDLLDLDDVFDCNNNNVERIIIEDTLTSINEDVYEVISI 828          

HSP 2 Score: 36.5798 bits (83), Expect = 2.130e-21
Identity = 28/29 (96.55%), Postives = 28/29 (96.55%), Query Frame = 3
Query:  324 MIPATYPIIILDDIVDDAPTCIDGDDIVD 410
            MIPATYPIIILDDIVDDAPTCIDGD IVD
Sbjct:  832 MIPATYPIIILDDIVDDAPTCIDGDAIVD 860          
BLAST of SMED30013626 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 51.6026 bits (122), Expect = 3.330e-13
Identity = 26/32 (81.25%), Postives = 26/32 (81.25%), Query Frame = 1
Query:  163 DVFDCNNNNVERIIIEDTPTSINEDVYEVISI 258
               DC NNNVERII EDTPTSINE VYEVISI
Sbjct:  458 QTMDCINNNVERIIFEDTPTSINEVVYEVISI 489          

HSP 2 Score: 39.2762 bits (90), Expect = 3.330e-13
Identity = 29/29 (100.00%), Postives = 29/29 (100.00%), Query Frame = 3
Query:  324 MIPATYPIIILDDIVDDAPTCIDGDDIVD 410
            MIPATYPIIILDDIVDDAPTCIDGDDIVD
Sbjct:  495 MIPATYPIIILDDIVDDAPTCIDGDDIVD 523          
BLAST of SMED30013626 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 51.6026 bits (122), Expect = 3.413e-13
Identity = 26/32 (81.25%), Postives = 26/32 (81.25%), Query Frame = 1
Query:  163 DVFDCNNNNVERIIIEDTPTSINEDVYEVISI 258
               DC NNNVERII EDTPTSINE VYEVISI
Sbjct:  449 QTMDCINNNVERIIFEDTPTSINEVVYEVISI 480          

HSP 2 Score: 39.2762 bits (90), Expect = 3.413e-13
Identity = 29/29 (100.00%), Postives = 29/29 (100.00%), Query Frame = 3
Query:  324 MIPATYPIIILDDIVDDAPTCIDGDDIVD 410
            MIPATYPIIILDDIVDDAPTCIDGDDIVD
Sbjct:  486 MIPATYPIIILDDIVDDAPTCIDGDDIVD 514          
BLAST of SMED30013626 vs. Planmine SMEST
Match: SMESG000046659.1 (SMESG000046659.1)

HSP 1 Score: 51.9878 bits (123), Expect = 6.430e-13
Identity = 26/27 (96.30%), Postives = 26/27 (96.30%), Query Frame = 1
Query:  178 NNNNVERIIIEDTPTSINEDVYEVISI 258
            NNNNVERIIIEDTP SINEDVYEVISI
Sbjct:  541 NNNNVERIIIEDTPNSINEDVYEVISI 567          

HSP 2 Score: 38.1206 bits (87), Expect = 6.430e-13
Identity = 28/29 (96.55%), Postives = 28/29 (96.55%), Query Frame = 3
Query:  324 MIPATYPIIILDDIVDDAPTCIDGDDIVD 410
            MIPATYPIIILDDIVDDAP CIDGDDIVD
Sbjct:  572 MIPATYPIIILDDIVDDAPNCIDGDDIVD 600          
The following BLAST results are available for this feature:
BLAST of SMED30013626 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30013626 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 SMED30013626 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 SMED30013626 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30013626 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 SMED30013626 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30013626 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 SMED30013626 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 SMED30013626 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30013626 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30013626 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 SMED30013626 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 SMED30013626 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30013626 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000055962.11.000e-2773.75SMESG000055962.1[more]
SMESG000017989.12.130e-2176.12SMESG000017989.1[more]
SMESG000058180.13.330e-1381.25SMESG000058180.1[more]
SMESG000058180.13.413e-1381.25SMESG000058180.1[more]
SMESG000046659.16.430e-1396.30SMESG000046659.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013626 ID=SMED30013626|Name=SMED30013626|organism=Schmidtea mediterranea sexual|type=transcript|length=411bp
AATTAATTCATAAATTTTAATATGGCAGGACAAAATAATATTTTAAGAAG
TCTTCTAACTTCATCCATTGGTAATTTTTATTTATTATTTATTACCATTA
ATCTTTTAGTAAATTTAGACTGGTTCGATGTAACCGAAAATGAGGATCTT
TTGGATTTGGATGACGTTTTTGATTGTAATAATAATAATGTTGAAAGAAT
TATTATTGAAGATACTCCCACTTCAATTAATGAAGATGTTTATGAGGTTA
TATCTATCGGTAAGTTTAATATTTATTTATTTTCAAAATATAAAAAAAAA
ACATTTCAGATGATGATGATGATATGATTCCGGCAACTTACCCAATAATT
ATTTTGGATGATATAGTGGATGATGCCCCCACTTGTATTGATGGAGATGA
TATAGTGGATA
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protein sequence of SMED30013626-orf-1

>SMED30013626-orf-1 ID=SMED30013626-orf-1|Name=SMED30013626-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
MAGQNNILRSLLTSSIGNFYLLFITINLLVNLDWFDVTENEDLLDLDDVF
DCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTFQMMMM
I*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 7..29