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.t21 TTS g5009.t21 6409506 6409506
chr_2 g5009 g5009.t21 isoform g5009.t21 6409605 6421462
chr_2 g5009 g5009.t21 exon g5009.t21.exon1 6409605 6409964
chr_2 g5009 g5009.t21 cds g5009.t21.CDS1 6409818 6409964
chr_2 g5009 g5009.t21 exon g5009.t21.exon2 6411092 6411157
chr_2 g5009 g5009.t21 cds g5009.t21.CDS2 6411092 6411157
chr_2 g5009 g5009.t21 exon g5009.t21.exon3 6411368 6411551
chr_2 g5009 g5009.t21 cds g5009.t21.CDS3 6411368 6411551
chr_2 g5009 g5009.t21 exon g5009.t21.exon4 6411616 6411781
chr_2 g5009 g5009.t21 cds g5009.t21.CDS4 6411616 6411781
chr_2 g5009 g5009.t21 exon g5009.t21.exon5 6411845 6412078
chr_2 g5009 g5009.t21 cds g5009.t21.CDS5 6411845 6412078
chr_2 g5009 g5009.t21 exon g5009.t21.exon6 6412150 6412302
chr_2 g5009 g5009.t21 cds g5009.t21.CDS6 6412150 6412302
chr_2 g5009 g5009.t21 exon g5009.t21.exon7 6413085 6413216
chr_2 g5009 g5009.t21 cds g5009.t21.CDS7 6413085 6413216
chr_2 g5009 g5009.t21 exon g5009.t21.exon8 6413876 6413950
chr_2 g5009 g5009.t21 cds g5009.t21.CDS8 6413876 6413918
chr_2 g5009 g5009.t21 exon g5009.t21.exon9 6421285 6421462
chr_2 g5009 g5009.t21 TSS g5009.t21 6421462 6421462

Sequences

>g5009.t21 Gene=g5009 Length=1548
AGTTTTACTTTAGACTCGAATATAGTCAGTCACCTTAAAATTTTGCTGGCAATCTATATT
AACAACTTGATAAAAAAAATATTTTACAACCACAACAGATTAAGAGCAAAAAATACGACA
CAAATTAATTTTGAAAAAAAAAAATACTACGAAAAATCCATAAAGCAATTTAAATTAGGT
GAACTCAGTAACAACGACTACGGTGACACAATGCGACGTCAAAGCGATGATTATAAAACA
CACTATTTACCAGATGTAAGTGAAGAAAGCGAATATGACTTGCTATATGACCGTTTTGGA
CTTGGTTATCGCTCATCTAAATCTAAATCACAATCACCTGATCCATTTCGATTGTACAAG
TATTCGCCCGATCGCAAAAGTTCAAATCATGGAGCAGATTTAACGACAGACACAGATAGT
TTTATGATAGGAAATCGAGTTTATGTTGGAGGAGTTAAACCCGGTCGTATTACTTTTATT
GGCGAAGTTCATTTCGCCCCGGGTGAATGGGCTGGAGTTGTTTTAGATGAGCCAGAAGGC
AAAAATGATGGTGCAGTTAGTGGAAAACGCTATTTTCAGTGTGAACCTAAAAAGGGAATA
TTTTCACGCCTCACACGACTAACTCGTGAACCATTATCATCAACCACAACTGATGGTCCA
TTAAGTACAGATTATAGCTTCCGTTCATTTACATCACCACTTCGAAACACATCGGGAAAT
ACATCACCAACACAGAGTGTTTCTAGTGTCTCTAAAACAGCAGCTGGAACAAAAATTATT
CCCGAAATAAATGATCGTGTTATTGTCAAGAGTGCAACTGGAAGTCGTGCTGGAATTCTT
CGTTATCGTGGAGAGCCAGCATTTGCTAGTGGTATTTGGTGTGGTGTTGAATATGAAGAG
CCTGTTGGCAAAAATGACGGATCAGTTAGTGGACAAAGATATTTCAAATGCGCACCCAAT
CATGGAATTTTTGTGCCTGAAGGAAAGGTTGTTTTATCACCATTAGCACGAAAAATGCGC
CTTTCAAGACAAAATTCACAAGAATCGTTAACATCAAACATTACACTTAACAGCTTGGCT
TCGACAAATACTTCAAAATTGCGGTTAAATGCAACACAAAAGCGCCTATCGACACTTAAT
AAGTCACCATCGGCAACGTCAACACCAAAACCCTCGTTCTCGTTGCAGGACATTTTACGA
GAGAAATCGAATCATATTGAACAAATCATGAAAGAACGAGATATTGAACGTGAAGAAATG
GCAGCTCAAACAGTTCTTTATCAAAAGAATCTTAATCAGGTAAAATTTCTTGTACAATTA
ATTTGTTTTTTTTAGCTTGAACATTTTTTTATCTGTGTCTGCGTCTGAACAAAGACATTG
TCTTATTTACAAAAGAGTCCAAGTCCTGACGTTGAAGAACATATTGGAAGATGGGCTACA
TATATTCGACAGAGAAGTGAACACATTGATGACTTGAGACGACAATTCACAGGTTGGACT
GGCAATCACGAGAGACATTGCATTCTTCATGATGTCTTTTTGACATAA

>g5009.t21 Gene=g5009 Length=374
MRRQSDDYKTHYLPDVSEESEYDLLYDRFGLGYRSSKSKSQSPDPFRLYKYSPDRKSSNH
GADLTTDTDSFMIGNRVYVGGVKPGRITFIGEVHFAPGEWAGVVLDEPEGKNDGAVSGKR
YFQCEPKKGIFSRLTRLTREPLSSTTTDGPLSTDYSFRSFTSPLRNTSGNTSPTQSVSSV
SKTAAGTKIIPEINDRVIVKSATGSRAGILRYRGEPAFASGIWCGVEYEEPVGKNDGSVS
GQRYFKCAPNHGIFVPEGKVVLSPLARKMRLSRQNSQESLTSNITLNSLASTNTSKLRLN
ATQKRLSTLNKSPSATSTPKPSFSLQDILREKSNHIEQIMKERDIEREEMAAQTVLYQKN
LNQVKFLVQLICFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5009.t21 Coils Coil Coil 329 349 -
7 g5009.t21 Gene3D G3DSA:2.30.30.190 - 53 147 4.1E-31
8 g5009.t21 Gene3D G3DSA:2.30.30.190 - 167 268 8.4E-28
3 g5009.t21 PANTHER PTHR18916:SF79 RESTIN HOMOLOG 57 365 7.5E-88
4 g5009.t21 PANTHER PTHR18916 DYNACTIN 1-RELATED MICROTUBULE-BINDING 57 365 7.5E-88
1 g5009.t21 Pfam PF01302 CAP-Gly domain 73 136 6.5E-22
2 g5009.t21 Pfam PF01302 CAP-Gly domain 193 260 2.3E-23
11 g5009.t21 ProSitePatterns PS00845 CAP-Gly domain signature. 91 122 -
10 g5009.t21 ProSitePatterns PS00845 CAP-Gly domain signature. 214 245 -
15 g5009.t21 ProSiteProfiles PS50245 CAP-Gly domain profile. 91 133 17.73
14 g5009.t21 ProSiteProfiles PS50245 CAP-Gly domain profile. 214 256 18.036
13 g5009.t21 SMART SM01052 CAP_GLY_2 73 138 1.4E-28
12 g5009.t21 SMART SM01052 CAP_GLY_2 193 261 4.4E-31
6 g5009.t21 SUPERFAMILY SSF74924 Cap-Gly domain 51 155 4.06E-33
5 g5009.t21 SUPERFAMILY SSF74924 Cap-Gly domain 192 276 2.75E-29

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5009/g5009.t21; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t21.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