SMED30023731

Overview
NameSMED30023731
Smed IDSMED30023731
Length (bp)403
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 SMED30023731 (SMED30023731) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023731 (SMED30023731) 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
SMED30023731 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.029196:7956..8339 +1762
v31.030758:1335..1721 -1742
v31.039770:1614..1996 -1741
v31.036796:2767..3148 +1734
v31.004765:46424..46811 +1734
v31.001977:914..1301 -1734
v31.039809:887..1272 +1729
v31.029808:5806..6190 -1727
v31.024145:11878..12263 +1726
v31.031566:1467..1853 -1725
v31.030769:2292..2721 -1721
v31.010250:2412..2801 -1720
v31.041907:1431..1813 -1718
v31.030317:1897..2282 -1717
v31.007937:37087..37506 +1716
v31.000146:228894..229280 +1716
v31.011596:16616..17037 +1712
v31.000234:101012..101397 -1710
v31.022608:8175..8559 +1709
v31.003181:47564..47943 -1709
v31.009462:760..1144 -1708
v31.000110:1513..1896 -1708
v31.043798:1280..1658 -1705
v31.047726:1516..1935 +1699
v31.033292:3375..3794 -1699
v31.001204:69920..70300 -1699
v31.040662:1811..2270 -1695
v31.035763:1774..2190 +1693
v31.029230:4544..4924 +1691
v31.003451:40444..40862 -1690
v31.035502:3146..3614 +1689
v31.016334:3745..4137 -1689
v31.041292:2206..2593 +1687
v31.035246:391..810 -1687
v31.007032:18650..19030 +1681
v31.002579:60397..61672 -1681
v31.001780:49301..49725 -1681
v31.007326:30242..30618 +1680
v31.045459:347..766 +1679
v31.000131:268..689 +1678
v31.036881:1158..1582 -1676
v31.013000:2009..2839 -1666
v31.024943:3073..3502 +1665
v31.002960:88699..89080 +1664
v31.007740:13117..13497 -1663
v31.014450:18691..19113 +1657
v31.003882:68035..68417 -1653
v31.001147:23670..24091 +1647
v31.045634:1820..2200 +1645
v31.020290:195..576 -1645
v31.027461:4055..4476 -1643
v31.008072:1146..1513 -1642
v31.010689:22976..23398 -1639
v31.003799:39766..40451 -1636
v31.008947:33790..34209 +1630
v31.007414:34316..34698 +1629
v31.002634:50304..50685 -1627
v31.000893:103546..103925 -1627
v31.012697:12936..13432 -1625
v31.029377:2888..3384 +1622
v31.003859:37523..37980 -1622
v31.011902:19033..19413 -1618
v31.000559:24613..25109 +1618
v31.008453:18642..19060 +1616
v31.000151:7736..8197 -1614
v31.018238:13061..13480 +1612
v31.010150:1542..1955 +1605
v31.025155:3747..4106 +1603
v31.003260:6166..6585 -1603
v31.021537:5608..6027 -1602
v31.031857:3560..3981 -1600
v31.001692:50472..50852 -1600
v31.002501:3195..3691 +1599
v31.000328:73431..73927 -1599
v31.001528:18649..19023 +1597
v31.001255:24432..24845 -1595
v31.000816:98261..98678 +1595
v31.004799:24429..24883 -1594
v31.003844:37091..37510 +1594
v31.000623:191..571 -1591
v31.000057:124368..124748 +1591
v31.000670:26387..26803 -1587
v31.003473:1172..1629 -1586
v31.023715:2165..2584 +1567
v31.004474:39957..40336 -1564
v31.000006:92566..93062 -1563
v31.027160:5169..5513 +1561
v31.001699:23946..24364 +1560
v31.009184:1154..1530 -1557
v31.000237:168098..168598 -1554
v31.016646:10156..10522 -1552
v31.012793:4191..4680 +1550
v31.005234:46823..47245 +1540
v31.006302:5930..6301 +1537
v31.002523:11818..12271 -1533
v31.009483:5343..5759 +1531
v31.020608:6153..6532 -1529
v31.032867:3239..3587 +1526
v31.049374:1757..2146 -1525
v31.000302:83889..84336 +1523
v31.010651:3671..4027 -1521
v31.022329:7065..7436 +1517
v31.014919:1845..2209 +1511
v31.006578:22393..22764 +1500
v31.013481:17355..17753 +1499
v31.009201:20541..20951 -1497
v31.000352:56515..56891 +1495
v31.003903:34943..35317 -1491
v31.015411:5483..5840 -1485
v31.001019:15347..15721 +1483
v31.002609:34937..35297 -1466
v31.000634:62692..63099 +1463
v31.000606:40400..40773 -1454
v31.027545:6568..6947 -1452
v31.011885:4182..4594 +1447
v31.002976:74205..74599 +1447
v31.016681:17919..18338 +1445
v31.025838:960..1367 +1444
v31.010184:9359..9740 +1442
v31.023032:1476..1850 -1440
v31.021298:8989..9363 +1440
v31.004844:49461..49830 +1433
v31.017968:16244..16619 +1432
v31.018697:274..681 -1427
v31.006826:8011..8380 -1424
v31.007197:13412..13780 +1420
v31.005817:11046..11398 +1416
v31.000389:112816..113223 +1416
v31.000486:101120..101474 +1414
v31.011678:14584..14959 +1405
v31.003112:34930..35298 -1403
v31.013023:12430..12840 +1400
v31.018981:2906..3309 -1399
v31.013806:5022..5392 +1397
v31.017939:8808..9187 +1395
v31.017092:10882..11320 -1376
v31.001442:1619..1983 +1373
v31.005272:7020..7383 +1365
v31.035178:560..928 +1348
v31.044043:684..1062 -1339
v31.008365:31134..31538 -1335
v31.001371:25689..26062 +1335
v31.011344:11289..11672 +1334
v31.015796:848..1231 +1316
v31.011726:1541..1864 -1310
v31.000164:136494..136874 +1304
v31.000719:14939..15253 -1294
v31.001452:33344..33733 -1293
v31.005584:29292..29675 -1291
v31.020828:1295..1674 +1285
v31.003893:2984..3361 -1267
v31.025562:3817..4197 +1260
v31.041781:4026..4398 -1255
v31.010129:18759..19140 +1246
v31.001553:36952..37353 +1227
v31.029460:865..1243 +1221
v31.003467:33507..33889 +1220
v31.021238:8000..8357 -1219
v31.000570:142614..142987 -1213
v31.028255:1390..1768 -1212
v31.010429:1531..1906 +1210
v31.035640:3061..3434 +1204
v31.007382:698..1080 -1202
v31.001681:1263..1645 -1202
v31.000227:92154..92536 -1198
v31.020869:13053..13426 +1195
v31.012944:16194..16567 -1195
v31.003693:66381..66754 -1195
v31.006098:1980..2352 -1192
v31.029571:884..1263 -1190
v31.003683:46466..46847 -1189
v31.025387:3613..3983 -1187
v31.004151:38218..38587 -1186
v31.008607:1484..1863 -1182
v31.000018:175510..175886 -1179
v31.017806:12454..12825 +1178
v31.002649:82661..83040 +1178
v31.005431:457..837 +1175
v31.007643:13411..13789 +1172
v31.004115:57738..58109 -1172
v31.007415:28564..28937 +1168
v31.024810:4714..5087 +1167
v31.003875:32108..32481 +1167
v31.001595:31715..32091 +1162
v31.002008:6423..6799 -1160
v31.001162:72114..72490 +1160
v31.000018:127240..127611 +1160
v31.017448:8197..8577 +1159
v31.001966:1427..1806 +1155
v31.009363:21464..21845 -1154
v31.006992:11005..11384 +1154
v31.013852:14763..15142 +1153
v31.010862:19822..20194 -1153
v31.017951:2410..2780 +1152
v31.011601:9050..9431 -1152
v31.004136:49351..49717 -1149
v31.000225:8918..9318 -1146
v31.003631:15653..16065 +1124
v31.000863:26406..26767 +1123
v31.000139:180249..180621 +1116
v31.013645:13732..14100 -1105
v31.007418:13284..13654 +1101
v31.000735:44290..44666 +1099
v31.015979:11951..12319 +1096
v31.014718:3194..3569 -1096
v31.006396:16239..16609 -1094
v31.025768:3644..4055 +1086
v31.001441:9958..10338 +1081
v31.000296:107255..107624 +1080
v31.019209:1071..1465 -1079
v31.003687:28515..28884 +1074
v31.014233:11204..11578 +1055
v31.026522:1829..2202 +1039
v31.012744:9674..10038 -1034
v31.003351:40606..40973 -975
v31.000479:164857..165222 +953
v31.019311:12358..12754 +934
v31.012694:22787..23150 +930
v31.000733:113471..114009 -855
v31.000479:164805..165184 +767
v31.008648:1173..1553 +633
v31.008648:1204..1553 +624
v31.003693:66413..66787 -614
v31.019209:1109..1498 -609
v31.005584:29324..29708 -609
v31.020828:1262..1642 +591
v31.020869:13020..13394 +589
v31.007415:28538..28905 +588
v31.000733:113386..113785 +580
v31.017951:2372..2742 +573
v31.024810:4655..5055 +567
v31.006098:2012..2412 -565
v31.017448:8139..8539 +548
v31.004151:38250..38609 -547
v31.006992:10989..11346 +544
v31.035640:3081..3402 +541
v31.000227:92192..92554 -539
v31.010862:19854..20192 -534
v31.011601:9088..9455 -532
v31.006396:16277..16668 +531
v31.000164:136476..136842 +530
v31.001595:31721..32059 +527
v31.008607:1522..1848 -524
v31.003467:33491..33851 +522
v31.004115:57769..58120 -519
v31.003875:32090..32449 +516
v31.001681:1301..1661 -516
v31.007643:13426..13751 +513
v31.012694:22702..23112 +511
v31.007382:736..1096 -507
v31.009363:21502..21831 -505
v31.026522:1770..2164 -504
v31.049374:1725..2109 -500
v31.029571:922..1274 -491
v31.001966:1457..1768 +490
v31.008648:978..1449 +459
v31.024943:3041..3395 -441
v31.014233:11204..11540 +437
v31.016681:17887..18228 -427
v31.035246:491..842 +426
v31.012793:4159..4513 -426
v31.001780:49407..49757 +423
v31.001019:15383..15759 +404
Homology
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000017989.1 (SMESG000017989.1)

HSP 1 Score: 95.1301 bits (235), Expect = 1.732e-23
Identity = 64/88 (72.73%), Postives = 65/88 (73.86%), Query Frame = -1
Query:   83 LLDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPTC 346
            + DCNNNNVERIIIEDT TSINEDVYEVISI                    DDDMIPATYPIIILDDIVDDAPTCIDGD IVDNAPTC
Sbjct:  798 VFDCNNNNVERIIIEDTLTSINEDVYEVISI--------------------DDDMIPATYPIIILDDIVDDAPTCIDGDAIVDNAPTC 865          
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000046659.1 (SMESG000046659.1)

HSP 1 Score: 88.5817 bits (218), Expect = 2.981e-21
Identity = 61/84 (72.62%), Postives = 62/84 (73.81%), Query Frame = -1
Query:   83 NNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPTC 334
            NNNNVERIIIEDTP SINEDVYEVISI                   DDD MIPATYPIIILDDIVDDAP CIDGDDIVD+APTC
Sbjct:  541 NNNNVERIIIEDTPNSINEDVYEVISI-------------------DDDYMIPATYPIIILDDIVDDAPNCIDGDDIVDDAPTC 605          
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000046659.1 (SMESG000046659.1)

HSP 1 Score: 88.1965 bits (217), Expect = 3.758e-21
Identity = 61/84 (72.62%), Postives = 62/84 (73.81%), Query Frame = -1
Query:   83 NNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPTC 334
            NNNNVERIIIEDTP SINEDVYEVISI                   DDD MIPATYPIIILDDIVDDAP CIDGDDIVD+APTC
Sbjct:  515 NNNNVERIIIEDTPNSINEDVYEVISI-------------------DDDYMIPATYPIIILDDIVDDAPNCIDGDDIVDDAPTC 579          
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 84.3445 bits (207), Expect = 9.209e-20
Identity = 63/86 (73.26%), Postives = 65/86 (75.58%), Query Frame = -1
Query:   86 LDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 343
            +DC NNNVERII EDTPTSINE VYEVISI                  +DDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT
Sbjct:  460 MDCINNNVERIIFEDTPTSINEVVYEVISI------------------DDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 527          
BLAST of SMED30023731 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 84.3445 bits (207), Expect = 9.847e-20
Identity = 63/86 (73.26%), Postives = 65/86 (75.58%), Query Frame = -1
Query:   86 LDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNIYLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 343
            +DC NNNVERII EDTPTSINE VYEVISI                  +DDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT
Sbjct:  451 MDCINNNVERIIFEDTPTSINEVVYEVISI------------------DDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAPT 518          
The following BLAST results are available for this feature:
BLAST of SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 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 SMED30023731 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017989.11.732e-2372.73SMESG000017989.1[more]
SMESG000046659.12.981e-2172.62SMESG000046659.1[more]
SMESG000046659.13.758e-2172.62SMESG000046659.1[more]
SMESG000058180.19.209e-2073.26SMESG000058180.1[more]
SMESG000058180.19.847e-2073.26SMESG000058180.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023731 ID=SMED30023731|Name=SMED30023731|organism=Schmidtea mediterranea sexual|type=transcript|length=403bp
GTCAAATAAAGTTTAAAAAATAAATAAATTACTAACATAAATCTGCATCA
ATATTATCATCAGATGAATCGTCAACATCAATACAAGTGGGGGCATTATC
CACTATATCATCTCCATCAATACAAGTGGGGGCATCATCCACTATATCAT
CCAAAATAATTATTGGGTAAGTTGCCGGAATCATATCATCATCATCATTT
GAAATGTTTGTTTTTTTTTTATATTTTGAAAATAAATAAATATTAAACTT
ACCGATAGATATAACCTCATAAACATCTTCATTAATTGAAGTGGGAGTAT
CTTCAATAATAATTCTTTCAACATTATTATTATTACAATCTAAAAGAATA
TTAATAAAATCATAAACAAATTTACTAACTTTCTCCATTGACGCTTTTGT
TCA
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protein sequence of SMED30023731-orf-1

>SMED30023731-orf-1 ID=SMED30023731-orf-1|Name=SMED30023731-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MEKVSKFVYDFINILLDCNNNNVERIIIEDTPTSINEDVYEVISIGKFNI
YLFSKYKKKTNISNDDDDMIPATYPIIILDDIVDDAPTCIDGDDIVDNAP
TCIDVDDSSDDNIDADLC*
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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: 10..32