Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytospin-A.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g2780 g2780.t1 isoform g2780.t1 20219906 20226015
chr_3 g2780 g2780.t1 exon g2780.t1.exon1 20219906 20220388
chr_3 g2780 g2780.t1 cds g2780.t1.CDS1 20219906 20220388
chr_3 g2780 g2780.t1 exon g2780.t1.exon2 20220746 20221066
chr_3 g2780 g2780.t1 cds g2780.t1.CDS2 20220746 20221066
chr_3 g2780 g2780.t1 exon g2780.t1.exon3 20221127 20222095
chr_3 g2780 g2780.t1 cds g2780.t1.CDS3 20221127 20222095
chr_3 g2780 g2780.t1 exon g2780.t1.exon4 20222179 20222488
chr_3 g2780 g2780.t1 cds g2780.t1.CDS4 20222179 20222488
chr_3 g2780 g2780.t1 exon g2780.t1.exon5 20222586 20223839
chr_3 g2780 g2780.t1 cds g2780.t1.CDS5 20222586 20223839
chr_3 g2780 g2780.t1 exon g2780.t1.exon6 20224193 20224678
chr_3 g2780 g2780.t1 cds g2780.t1.CDS6 20224193 20224678
chr_3 g2780 g2780.t1 exon g2780.t1.exon7 20225224 20225349
chr_3 g2780 g2780.t1 cds g2780.t1.CDS7 20225224 20225349
chr_3 g2780 g2780.t1 exon g2780.t1.exon8 20225414 20225543
chr_3 g2780 g2780.t1 cds g2780.t1.CDS8 20225414 20225543
chr_3 g2780 g2780.t1 exon g2780.t1.exon9 20225716 20225860
chr_3 g2780 g2780.t1 cds g2780.t1.CDS9 20225716 20225860
chr_3 g2780 g2780.t1 exon g2780.t1.exon10 20225920 20226015
chr_3 g2780 g2780.t1 cds g2780.t1.CDS10 20225920 20226015
chr_3 g2780 g2780.t1 TTS g2780.t1 20226544 20226544
chr_3 g2780 g2780.t1 TSS g2780.t1 NA NA

Sequences

>g2780.t1 Gene=g2780 Length=4320
ATGATCAAATTGAAATCATTGTTTCGTAGAGGACAAAGTGGAAGTCCATCTGCATCATCA
AGTTCATCAAAACAAAATCAGCAAATATCGCCTGCACATTCTAATTCTATTGGTCTTAAG
ACATCAGCTTCTGCATCAAGTCTTGATCGAGTTGAATTTAATAACACTGGTAGTGCTTCG
AATGAACTTGGTGCAACAAGGAAATTATCAAAGGGTCAAAAACAATCTTCAAAAGATAAA
TTGAATGATTTACTGCGAGTCGCATCCAAGGAAAAGTTGATTGATGAAAAGAAAGAGTTG
AAGAAGCAACAGAAATTACAGCAAAAACAAATGCAGCAAGTTGCTCAACAGTCGACAAAT
GTCCACCATATACCATCATCATCGTCTGTAGCTACAGCAACTGGACATTTGCCAAACAAT
CAACTCTCAGGTCGTTCAAACTCTAAAGATTTTGATGTCGTTACATATGATGAAGTTCAA
GACATAAGACATAAGAAAACTATGCAAGAACTCCTTCAATTGCAACAGGAAAATGCAAGT
TTGGAAATCAAGATTAAAGAACTAACGACATCACATAACGAATTATTGCTGCTGCGCAAA
GACATTCAGAAACTTCAACAGACAAACGAAATGAATAATTCAAAGCTTAATCAACTAGAG
GAGGAGAACGAGTCATTACGAATGCGTTTGAGAAATGTTGTACAATCACCAATATCTGAC
TCTGAGAAACAGCAGATGATTGACGACGGAAGACAGAAACACAGTTCTTCTGCTCCTGCA
TCTATTTCAATGACTCTTCCTAATCTTGTACCAAATATAGAAATGGATGCATCTTGTACA
ACAACACCAGATTGGGATAAACAATCGTCGAGTAGTGAGGTCTCTGTAGCATGTTTGCAA
GACAAGATAATACAAATGGAGGAAACCCATCACTCAACCAATGAAGAATTACAAGCTACT
CTTCAAGAGCTCGCTGATCTACAAAATCAAGTACTGGAATTACAAAATGACAACGAACGC
CTATCAGACGAAAAGGATGTAATATTTCAAACACTTTGCCGTCAGACTGAAAAGCTCGAA
GATACTAGAAGTCAAGTCGAGACATTGCAAAAATTATTGCTTCGTGATCCAAACAATCAG
CCCGAATCTGCATCGTCAGAACGTGAACAAAAATTGATGGACTTATTGAAAAATGCACAA
GAAGAGAGAGAGGCTTTAATGATAAAATTAGAGGAATTGAATTCGGAATTGCAAGAAAAA
AGTCAATTGACTGAGTCATACCTAATGGATACTAATCGTTTGAAAGAAAGAATCAGTGTC
CTCGAATCAACTGTTGATGCTTCAACCGCTGATCGAAAGGAAATTGAAAGACAATTATGT
GCAACAAAAGAGGAAGCATCCTCAAAACAAATTGAAATAAGCCGTTTGACGACTCTATTA
GAAAATGCACGCTCTAAAATTGAAGAAATTGAACAAGATAGAGCTTTAGGTGAGAAATCA
GACTTGGGCGAGTTGTTAGATAATGCACGAAAGGAAAAAGATTATCTCGAGATTGAAATA
ACAAGCTTGCAAGAGCAATTGTCAAAGAGTCAAAACGAGACTCAAAAATTGCGTGATCAA
CTCGCTGGAATAACTGAAGAATGTAAAGTTACCCGCAACAATGCAAAATGTGCATTAAGT
GATTTGGAATACAAGTATGAACAACTAAAACAAGAGAAATTGAAAATTCAAGCCGATTAT
CAAATACTCGTAGACACAACTAACGAACTTCAAGTTCAAATAAAATGTCTGATAGAAGAT
AAAGCTCAATTGGAAACACTCTATTCAGAAACGCAACATCATTTAGTCGATATTGAGCGC
CAATTGTCTGAGACAAAAGAAAAGCTTGAAAGCGAAATTCGCGCAAGAAGAACAGAGAAT
GAAGAATGGGAACAATTTCAACAAGATCTTCTCGTCTCCGTTCGTGTTGCAAATGATTTC
AAAACAGAAGCTCAGCAAGCTCATGAGCAATTAGCACTTGATAATAAATTATTGCGTGAC
AAAATTCGCGGACTAGAGACACAGATTGAAAAACTTAATAAACCAAATATTGTTGAGTTG
CATCCTAAAATAAATCCAATACAAGAGACTACAATGCAAGAAAAAGATGGTGACGTAGGA
GCAGATGAGTTTCTATTAGAGTTGACAAGAATGAGAAATTCTTTAAATGCATTAACATTA
AAGAATTTTATGTTTGATAAAAATAATGGTGAAGAAGAAATTATAAGCATGGAGGTAAAA
GAAGTTCCTACATCAGAAGATGTAATTGATTCAACTTCTTCGACATCATTATTGAAGCAA
AAACCACCCGTTAGTTTCAGAAGAAATTTGTCATCTAAACATCGTCAAGATAGTAATAGG
ACACAAAGTGGCCTAATTAGTCAAGATGATGTTTTAAAAGCATTAAACGAGAATCAAGAG
AAACTCAATGAGCAAACCAAATTAAAATCCAAAGTTCATTTTGCTGTAGAAGAACAGGAA
GATGAAAAAGTAAAAAAACAACTGAAATTATTAAAAGATTCTTCGCGCGAGTCAGATGAA
GTGGCAATAATAAATGAATTACCATGGCAAAAGAAGAGTTATCGAGAACATAAAACTGTT
ACTCCATACTTTAAACAAAGTAATAAACATGATAATCAAATTAAAGCGTTGAGTAATGAA
AATATGAAACAAATGCCAAAGGAAATAACTTTCCGGCCAATAGAAAGCAGTAAGAGTACT
GAAGATATTGATAAGCAACTAAAGCAAATTGTTAGACCTGTTCCATTATTTGCGTCGAAA
AGTTATCAAGAATTATCGACCACCAATGAAGGTTTTAAGCCACTCGATGAATTTATTACT
AAATCAAGCGATAATCTTTTGTTGGATAATATCGATGGAACACGTCGTATGAAAGAAAGT
AAAACACATAAATTGTTGCGAATTCGAAGTGCGAGTAATAATAGTCTCGATCGATCGAAT
GAACAGATTATTTATGAGAACTTTGACTATGAAGTTCCACTTTCCAATGATTTTGTTACA
ATGAGAAAAAAACAAAAGCCACCTTTACCACAACCAAGATTAAGTGGCGAGATAAATAAC
AACAGTCATAAGAATAAGGCTAACGAAGATGATAATAATTCTAAACGTAAATCCAAAACA
ATTGTTTATGTTTTGGATAAAGAAAAAGATGAATTTGTGCTAGAAAATCCTGAAATAGTT
GATGATGAAGCATATGAGAACATATTGTTTGAAAACAGCATCGATAAATATAGTGAATTC
GATTTGTTTAACACACTTCTAAACTCGCGTGATGATTTGGTAACATCTTCTAACGAATCA
CAACAATCAATATTGACGACAGTGCAGCAAGAAATGGCTCAACGAAGAAAACAAAAAAGT
AACGGAAGTACAGTAAAAAATGGAACTAGCAATTCTATTGGCAGCAACAACAACAATATC
AACAACACCACTATCACAAATAACAGTAATAATGGTATTGTGGCAAATTCAGTTTCTTAT
ATAACGCGACAAGATTCACGATTGTCTGTAAAAAGTTTGATTGAGAGCATCGAGAATACT
TCAAAGCAGACCAAAGTTTCGTCGTCTGGATCACAATCGGGATCGCAAACGAGTCTAAAC
AACTTGTCCGTTATAGAGCAGCAGCAGTGTGAAAAGTTAACAACAAACATTGATGAAGAG
AAGCAACAAAAGAATTTGAATAATAATTCCATCACGAGTAATCACAGCAATATTCTTACT
ACGTCAAATAATGTTAATTTGAATGGAACGCAAAAGAGTGGAGTGGCAATTCCACAAAAG
ACTGATGATCATGATCAATTCTATTCATCGATTTTAACATCACACAAGCACGATTACAAT
TTAAACCACAAACACGATTATGTGAGACGAAACAGCTACGGTGATATAAGCGAACGAAAA
GATCCATTAAATGCACTAGTGAAGAATGGCGGGTCGAAACGAAATGCTTTACTCAAATGG
TGTCAAAATAAAGTTGTTGGGTATCGAAATATCGACATAACCAACTTCAGTTCATCATGG
AATGATGGTTTGGCTTTATGTGCTCTAATGCATTCATATTTACCTGAAAAAATTCCATAT
GACGAACTTACACCACTTGACAAGAAGAAAAATTTTAGTTTAGCCTTCGATGCTGCAGAA
ACAGTTGGAATTAAGACAACTTTGAATATCAATGAAATGTGTCAACAGGAAAGACCAGAT
TGGCAATCAATAATGTCATATGTGACACAAATTTACAAGCATTTTGAGTCGCAGCCCTAA

>g2780.t1 Gene=g2780 Length=1439
MIKLKSLFRRGQSGSPSASSSSSKQNQQISPAHSNSIGLKTSASASSLDRVEFNNTGSAS
NELGATRKLSKGQKQSSKDKLNDLLRVASKEKLIDEKKELKKQQKLQQKQMQQVAQQSTN
VHHIPSSSSVATATGHLPNNQLSGRSNSKDFDVVTYDEVQDIRHKKTMQELLQLQQENAS
LEIKIKELTTSHNELLLLRKDIQKLQQTNEMNNSKLNQLEEENESLRMRLRNVVQSPISD
SEKQQMIDDGRQKHSSSAPASISMTLPNLVPNIEMDASCTTTPDWDKQSSSSEVSVACLQ
DKIIQMEETHHSTNEELQATLQELADLQNQVLELQNDNERLSDEKDVIFQTLCRQTEKLE
DTRSQVETLQKLLLRDPNNQPESASSEREQKLMDLLKNAQEEREALMIKLEELNSELQEK
SQLTESYLMDTNRLKERISVLESTVDASTADRKEIERQLCATKEEASSKQIEISRLTTLL
ENARSKIEEIEQDRALGEKSDLGELLDNARKEKDYLEIEITSLQEQLSKSQNETQKLRDQ
LAGITEECKVTRNNAKCALSDLEYKYEQLKQEKLKIQADYQILVDTTNELQVQIKCLIED
KAQLETLYSETQHHLVDIERQLSETKEKLESEIRARRTENEEWEQFQQDLLVSVRVANDF
KTEAQQAHEQLALDNKLLRDKIRGLETQIEKLNKPNIVELHPKINPIQETTMQEKDGDVG
ADEFLLELTRMRNSLNALTLKNFMFDKNNGEEEIISMEVKEVPTSEDVIDSTSSTSLLKQ
KPPVSFRRNLSSKHRQDSNRTQSGLISQDDVLKALNENQEKLNEQTKLKSKVHFAVEEQE
DEKVKKQLKLLKDSSRESDEVAIINELPWQKKSYREHKTVTPYFKQSNKHDNQIKALSNE
NMKQMPKEITFRPIESSKSTEDIDKQLKQIVRPVPLFASKSYQELSTTNEGFKPLDEFIT
KSSDNLLLDNIDGTRRMKESKTHKLLRIRSASNNSLDRSNEQIIYENFDYEVPLSNDFVT
MRKKQKPPLPQPRLSGEINNNSHKNKANEDDNNSKRKSKTIVYVLDKEKDEFVLENPEIV
DDEAYENILFENSIDKYSEFDLFNTLLNSRDDLVTSSNESQQSILTTVQQEMAQRRKQKS
NGSTVKNGTSNSIGSNNNNINNTTITNNSNNGIVANSVSYITRQDSRLSVKSLIESIENT
SKQTKVSSSGSQSGSQTSLNNLSVIEQQQCEKLTTNIDEEKQQKNLNNNSITSNHSNILT
TSNNVNLNGTQKSGVAIPQKTDDHDQFYSSILTSHKHDYNLNHKHDYVRRNSYGDISERK
DPLNALVKNGGSKRNALLKWCQNKVVGYRNIDITNFSSSWNDGLALCALMHSYLPEKIPY
DELTPLDKKKNFSLAFDAAETVGIKTTLNINEMCQQERPDWQSIMSYVTQIYKHFESQP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g2780.t1 CDD cd00014 CH 1335 1435 5.55587E-21
14 g2780.t1 Coils Coil Coil 90 117 -
20 g2780.t1 Coils Coil Coil 164 191 -
12 g2780.t1 Coils Coil Coil 202 236 -
13 g2780.t1 Coils Coil Coil 310 344 -
18 g2780.t1 Coils Coil Coil 389 423 -
19 g2780.t1 Coils Coil Coil 438 458 -
16 g2780.t1 Coils Coil Coil 473 547 -
15 g2780.t1 Coils Coil Coil 552 579 -
11 g2780.t1 Coils Coil Coil 587 646 -
17 g2780.t1 Coils Coil Coil 661 688 -
21 g2780.t1 Coils Coil Coil 805 825 -
10 g2780.t1 Gene3D G3DSA:1.10.418.10 - 1329 1438 7.5E-38
26 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 59 -
31 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 10 59 -
28 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 64 83 -
32 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 237 259 -
29 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 764 806 -
24 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 766 789 -
25 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 1022 1055 -
27 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 1128 1158 -
30 g2780.t1 MobiDBLite mobidb-lite consensus disorder prediction 1199 1221 -
3 g2780.t1 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 12 520 1.1E-171
6 g2780.t1 PANTHER PTHR23167:SF69 FI18193P1 12 520 1.1E-171
2 g2780.t1 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 515 694 1.1E-171
5 g2780.t1 PANTHER PTHR23167:SF69 FI18193P1 515 694 1.1E-171
4 g2780.t1 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 1196 1434 1.1E-171
7 g2780.t1 PANTHER PTHR23167:SF69 FI18193P1 1196 1434 1.1E-171
1 g2780.t1 Pfam PF00307 Calponin homology (CH) domain 1333 1436 8.5E-21
33 g2780.t1 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 1331 1436 24.289
23 g2780.t1 SMART SM00033 ch_5 1333 1431 3.4E-16
8 g2780.t1 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 1331 1435 2.62E-31
9 g2780.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 21 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

This gene does not belong to any pathways.

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values