Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytoplasmic dynein 1 intermediate chain.

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_1 g13860 g13860.t1 TSS g13860.t1 32879368 32879368
chr_1 g13860 g13860.t1 isoform g13860.t1 32879842 32885112
chr_1 g13860 g13860.t1 exon g13860.t1.exon1 32879842 32879984
chr_1 g13860 g13860.t1 cds g13860.t1.CDS1 32879842 32879984
chr_1 g13860 g13860.t1 exon g13860.t1.exon2 32880042 32880185
chr_1 g13860 g13860.t1 cds g13860.t1.CDS2 32880042 32880185
chr_1 g13860 g13860.t1 exon g13860.t1.exon3 32880245 32880375
chr_1 g13860 g13860.t1 cds g13860.t1.CDS3 32880245 32880375
chr_1 g13860 g13860.t1 exon g13860.t1.exon4 32881288 32881308
chr_1 g13860 g13860.t1 cds g13860.t1.CDS4 32881288 32881308
chr_1 g13860 g13860.t1 exon g13860.t1.exon5 32883462 32883638
chr_1 g13860 g13860.t1 cds g13860.t1.CDS5 32883462 32883638
chr_1 g13860 g13860.t1 exon g13860.t1.exon6 32883699 32883855
chr_1 g13860 g13860.t1 cds g13860.t1.CDS6 32883699 32883855
chr_1 g13860 g13860.t1 exon g13860.t1.exon7 32883927 32885112
chr_1 g13860 g13860.t1 cds g13860.t1.CDS7 32883927 32885112
chr_1 g13860 g13860.t1 TTS g13860.t1 32885311 32885311

Sequences

>g13860.t1 Gene=g13860 Length=1959
ATGGATAGAAAGGCCGAGCTTGAACGCAAAAAGGCAAAATTACAAGCCTTGCGTGATGAA
AAGGAAAAGAGGAGACGTGAGAAAGAAGAAAAGGACCTGCAGGAAGCTAAGGCTGGAGCT
CCTTCAGAAAAAGACACAAGAAAGGATTTAGATGAAATGTTGTCTTCTTTAGGTGTTGCC
CCAGTTTCTGAAGTTCTTTCATCACTTTCTTCTGTTACCTCTGTTACATCCGATCAGTCT
GGTCAAACGCCAGATGCTAGCCTTCAACCAACACTAAATGGACAAAATACGAAAGCAAAA
AAACAACAAACGCTATCAGTTGTACAAGTGCAGGTCACTAATATTCAACCAAAGGAGAAT
GTTACATATACAAAGCAGACACAAACGACAAGTTCAGGCACTCATGAGTTACGAGATGCA
CATGCAACCGATTATTATGTGCTTACTTTTGGGGACGCACAAGGCGATGACGAGGACCAT
TCGTTATCTCATTTGGATCATGGTGGATTTCATTCAAAATTACCTCCTGGAATTCTCCCT
CATGGTTTACCGACAGTCAAAGAAGTCGCTCCAGCAATTACACCACAAGAACAGAAGAAA
GATGATATTAAACAAGTAAAAGAACTTTCAGAAGAACAAAAGCAAATGATTATCTTATCA
GAGGATTTTCAACGTTTTGTTTTACGCTCTGGAAGAGTTATGGAACGCGCACTGTCAGAA
ACTGTTGATATTTATACAGATTATATAGGAGGTAGTGAATCTGATGAAGGACTAGATGAA
AAGTCTCATGCTCGGTTATCATTGAATCGAATATTTTACGATGACAGATGGTCAAAGAAT
CGTTGTGTTACATCATTTGATTGGTCAACCCATTTTCCTGAACTCATGGTCGCTTCTTAT
CACAATAACGAAGAATTACCAAATGAACCAGATGGCGTTGTTGTTGTTTGGAATACAAAA
TTTAAGAAACAAACACCTGAAGATGTTTTTCATTGTCAAAGTGCAGTCATGTCAACATGT
TTCGCTAAATTTCATCCTAATTTGATACTAGGTGGTACTTATTCAGGACAGATAGTACTG
TGGGATAATCGTGTTCAAAAGCGTACGCCAATACAACGAACACCACTTAGTTCGACTGCC
CATACTCATCCAGTCTATTGCTTGTCAATGGTGGGAACACAAAATGCTCATAATGTTATT
TCAATTTCGTCAGACGGTCGTTTATGTTCATGGAGTTTAGACATGTTATCAGCTCCTCAA
GATACTCTCGAATTACAACAAAAACAGCCAAAACCAATCGCAGTCACATGCATGTCATTC
CTTCATGATGAAGTCAATAATTTTGTATTAGGTAGTGAAGATGGATATGTGCATTCAGCA
TCGCGTCATGGTAATCGTTCGGGTATTATTGAAACTTATGAAAAACATTTAGGACCTGTA
ACAGGAATTTCAACTCATCAAAGTCATACTACTGCAGAGTTTTCACATTTATTCCTTACA
TCTTCAATTGATTGGACAATTAAATTGTGGAGTTTGAAAGACACAAAGCCACTTTATTCA
TTTGAAGACAATTCTGATTATGTGATGGATGTTGCTTGGTCGCCAATTCATCCATCTCTT
TTTGCGGCTGTTGATGGAAGTGGACGATTAGATTTGTGGAATTTGAATCAAGACACGGAA
GTGCCAACATGCTCAGTTGTTGTAGAAGGAGCTCCAGCATTAAATCGTGTTTCATGGACA
CCTTCAGGTTTGCATGTAACAATTGGTGATGAATCGGGCAAAATTTATGTTTATGATGTA
GCTGATAATGTAGCTCAGCCAAGAATGGATGAATGGCAACGGTTTGGAACAACATTACAT
GAATTAAAAATGAACACAAATGAAGACTTTGAAGATTTAGACAAATCAATGTCCATTCCA
CAACAACCTTTATCGCTGACAGGATCTTCTGTTGCGTAA

>g13860.t1 Gene=g13860 Length=652
MDRKAELERKKAKLQALRDEKEKRRREKEEKDLQEAKAGAPSEKDTRKDLDEMLSSLGVA
PVSEVLSSLSSVTSVTSDQSGQTPDASLQPTLNGQNTKAKKQQTLSVVQVQVTNIQPKEN
VTYTKQTQTTSSGTHELRDAHATDYYVLTFGDAQGDDEDHSLSHLDHGGFHSKLPPGILP
HGLPTVKEVAPAITPQEQKKDDIKQVKELSEEQKQMIILSEDFQRFVLRSGRVMERALSE
TVDIYTDYIGGSESDEGLDEKSHARLSLNRIFYDDRWSKNRCVTSFDWSTHFPELMVASY
HNNEELPNEPDGVVVVWNTKFKKQTPEDVFHCQSAVMSTCFAKFHPNLILGGTYSGQIVL
WDNRVQKRTPIQRTPLSSTAHTHPVYCLSMVGTQNAHNVISISSDGRLCSWSLDMLSAPQ
DTLELQQKQPKPIAVTCMSFLHDEVNNFVLGSEDGYVHSASRHGNRSGIIETYEKHLGPV
TGISTHQSHTTAEFSHLFLTSSIDWTIKLWSLKDTKPLYSFEDNSDYVMDVAWSPIHPSL
FAAVDGSGRLDLWNLNQDTEVPTCSVVVEGAPALNRVSWTPSGLHVTIGDESGKIYVYDV
ADNVAQPRMDEWQRFGTTLHELKMNTNEDFEDLDKSMSIPQQPLSLTGSSVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13860.t1 Coils Coil Coil 4 37 -
6 g13860.t1 Gene3D G3DSA:2.130.10.10 - 275 419 1.7E-14
5 g13860.t1 Gene3D G3DSA:2.130.10.10 - 420 627 1.6E-28
15 g13860.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 52 -
14 g13860.t1 MobiDBLite mobidb-lite consensus disorder prediction 66 101 -
2 g13860.t1 PANTHER PTHR12442:SF22 CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN-RELATED 3 625 8.8E-218
3 g13860.t1 PANTHER PTHR12442 DYNEIN INTERMEDIATE CHAIN 3 625 8.8E-218
1 g13860.t1 Pfam PF11540 Cytoplasmic dynein 1 intermediate chain 2 100 130 7.3E-11
16 g13860.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 311 608 15.188
10 g13860.t1 SMART SM00320 WD40_4 323 362 2.0
8 g13860.t1 SMART SM00320 WD40_4 372 412 4.1
12 g13860.t1 SMART SM00320 WD40_4 422 461 260.0
13 g13860.t1 SMART SM00320 WD40_4 466 511 0.012
11 g13860.t1 SMART SM00320 WD40_4 514 554 0.0029
9 g13860.t1 SMART SM00320 WD40_4 561 599 13.0
4 g13860.t1 SUPERFAMILY SSF50978 WD40 repeat-like 278 603 3.85E-40

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:0007018 microtubule-based movement BP
GO:0005515 protein binding MF
GO:0005868 cytoplasmic dynein complex CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following 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