Gene loci information

Transcript annotation

  • This transcript has been annotated as Restin-like protein.

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_2 g5009 g5009.t20 TTS g5009.t20 6409138 6409138
chr_2 g5009 g5009.t20 isoform g5009.t20 6409605 6421462
chr_2 g5009 g5009.t20 exon g5009.t20.exon1 6409605 6409778
chr_2 g5009 g5009.t20 cds g5009.t20.CDS1 6409605 6409778
chr_2 g5009 g5009.t20 exon g5009.t20.exon2 6409854 6409964
chr_2 g5009 g5009.t20 cds g5009.t20.CDS2 6409854 6409964
chr_2 g5009 g5009.t20 exon g5009.t20.exon3 6411092 6411157
chr_2 g5009 g5009.t20 cds g5009.t20.CDS3 6411092 6411157
chr_2 g5009 g5009.t20 exon g5009.t20.exon4 6411368 6411551
chr_2 g5009 g5009.t20 cds g5009.t20.CDS4 6411368 6411551
chr_2 g5009 g5009.t20 exon g5009.t20.exon5 6411616 6411781
chr_2 g5009 g5009.t20 cds g5009.t20.CDS5 6411616 6411781
chr_2 g5009 g5009.t20 exon g5009.t20.exon6 6411845 6412078
chr_2 g5009 g5009.t20 cds g5009.t20.CDS6 6411845 6412078
chr_2 g5009 g5009.t20 exon g5009.t20.exon7 6412150 6412302
chr_2 g5009 g5009.t20 cds g5009.t20.CDS7 6412150 6412302
chr_2 g5009 g5009.t20 exon g5009.t20.exon8 6413876 6413950
chr_2 g5009 g5009.t20 cds g5009.t20.CDS8 6413876 6413918
chr_2 g5009 g5009.t20 exon g5009.t20.exon9 6421285 6421462
chr_2 g5009 g5009.t20 TSS g5009.t20 6421462 6421462

Sequences

>g5009.t20 Gene=g5009 Length=1341
AGTTTTACTTTAGACTCGAATATAGTCAGTCACCTTAAAATTTTGCTGGCAATCTATATT
AACAACTTGATAAAAAAAATATTTTACAACCACAACAGATTAAGAGCAAAAAATACGACA
CAAATTAATTTTGAAAAAAAAAAATACTACGAAAAATCCATAAAGCAATTTAAATTAGGT
GAACTCAGTAACAACGACTACGGTGACACAATGCGACGTCAAAGCGATGATTATAAAACA
CACTATTTACCAGATCATGGAGCAGATTTAACGACAGACACAGATAGTTTTATGATAGGA
AATCGAGTTTATGTTGGAGGAGTTAAACCCGGTCGTATTACTTTTATTGGCGAAGTTCAT
TTCGCCCCGGGTGAATGGGCTGGAGTTGTTTTAGATGAGCCAGAAGGCAAAAATGATGGT
GCAGTTAGTGGAAAACGCTATTTTCAGTGTGAACCTAAAAAGGGAATATTTTCACGCCTC
ACACGACTAACTCGTGAACCATTATCATCAACCACAACTGATGGTCCATTAAGTACAGAT
TATAGCTTCCGTTCATTTACATCACCACTTCGAAACACATCGGGAAATACATCACCAACA
CAGAGTGTTTCTAGTGTCTCTAAAACAGCAGCTGGAACAAAAATTATTCCCGAAATAAAT
GATCGTGTTATTGTCAAGAGTGCAACTGGAAGTCGTGCTGGAATTCTTCGTTATCGTGGA
GAGCCAGCATTTGCTAGTGGTATTTGGTGTGGTGTTGAATATGAAGAGCCTGTTGGCAAA
AATGACGGATCAGTTAGTGGACAAAGATATTTCAAATGCGCACCCAATCATGGAATTTTT
GTGCCTGAAGGAAAGGTTGTTTTATCACCATTAGCACGAAAAATGCGCCTTTCAAGACAA
AATTCACAAGAATCGTTAACATCAAACATTACACTTAACAGCTTGGCTTCGACAAATACT
TCAAAATTGCGGTTAAATGCAACACAAAAGCGCCTATCGACACTTAATAAGTCACCATCG
GCAACGTCAACACCAAAACCCTCGTTCTCGTTGCAGGACATTTTACGAGAGAAATCGAAT
CATATTGAACAAATCATGAAAGAACGAGATATTGAACGTGAAGAAATGGCAGCTCAAACA
GTTCTTTATCAAAAGAATCTTAATCAGACATTGTCTTATTTACAAAAGAGTCCAAGTCCT
GACGTTGAAGAACATATTGGAAGATGGGCTACATATATTCGACAGAGAAGTGAACACATT
GATGACTTGAGACGACAATTCACAGGTTGGACTGGCAATCACGAGAGACATTGCATTCTT
CATGATGTCTTTTTGACATAA

>g5009.t20 Gene=g5009 Length=376
MRRQSDDYKTHYLPDHGADLTTDTDSFMIGNRVYVGGVKPGRITFIGEVHFAPGEWAGVV
LDEPEGKNDGAVSGKRYFQCEPKKGIFSRLTRLTREPLSSTTTDGPLSTDYSFRSFTSPL
RNTSGNTSPTQSVSSVSKTAAGTKIIPEINDRVIVKSATGSRAGILRYRGEPAFASGIWC
GVEYEEPVGKNDGSVSGQRYFKCAPNHGIFVPEGKVVLSPLARKMRLSRQNSQESLTSNI
TLNSLASTNTSKLRLNATQKRLSTLNKSPSATSTPKPSFSLQDILREKSNHIEQIMKERD
IEREEMAAQTVLYQKNLNQTLSYLQKSPSPDVEEHIGRWATYIRQRSEHIDDLRRQFTGW
TGNHERHCILHDVFLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5009.t20 Coils Coil Coil 285 305 -
8 g5009.t20 Gene3D G3DSA:2.30.30.190 - 25 108 5.0E-31
7 g5009.t20 Gene3D G3DSA:2.30.30.190 - 123 224 8.5E-28
3 g5009.t20 PANTHER PTHR18916:SF79 RESTIN HOMOLOG 12 324 3.6E-88
4 g5009.t20 PANTHER PTHR18916 DYNACTIN 1-RELATED MICROTUBULE-BINDING 12 324 3.6E-88
2 g5009.t20 Pfam PF01302 CAP-Gly domain 29 92 6.6E-22
1 g5009.t20 Pfam PF01302 CAP-Gly domain 149 216 2.3E-23
11 g5009.t20 ProSitePatterns PS00845 CAP-Gly domain signature. 47 78 -
10 g5009.t20 ProSitePatterns PS00845 CAP-Gly domain signature. 170 201 -
15 g5009.t20 ProSiteProfiles PS50245 CAP-Gly domain profile. 47 89 17.73
14 g5009.t20 ProSiteProfiles PS50245 CAP-Gly domain profile. 170 212 18.036
12 g5009.t20 SMART SM01052 CAP_GLY_2 29 94 1.4E-28
13 g5009.t20 SMART SM01052 CAP_GLY_2 149 217 4.4E-31
6 g5009.t20 SUPERFAMILY SSF74924 Cap-Gly domain 20 111 3.53E-32
5 g5009.t20 SUPERFAMILY SSF74924 Cap-Gly domain 148 230 2.36E-29

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5009/g5009.t20; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t20.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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