General information for g5009.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Restin-like protein.
Parent gene
- The parent gene g5009 is located on chr_2: 6422853..6423614 (- strand)
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.t4 | TTS | g5009.t4 | 6409506 | 6409506 |
| chr_2 | g5009 | g5009.t4 | isoform | g5009.t4 | 6409605 | 6422853 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon1 | 6409605 | 6409778 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS1 | 6409605 | 6409778 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS2 | 6409854 | 6409964 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS3 | 6411092 | 6411157 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS4 | 6411368 | 6411551 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon5 | 6411616 | 6411781 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS5 | 6411616 | 6411781 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon6 | 6411845 | 6412078 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS6 | 6411845 | 6412078 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon7 | 6412150 | 6412302 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS7 | 6412150 | 6412302 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon8 | 6412791 | 6412853 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS8 | 6412791 | 6412853 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon9 | 6413085 | 6413216 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS9 | 6413085 | 6413216 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon10 | 6413876 | 6413995 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS10 | 6413876 | 6413995 |
| chr_2 | g5009 | g5009.t4 | exon | g5009.t4.exon11 | 6422640 | 6422853 |
| chr_2 | g5009 | g5009.t4 | cds | g5009.t4.CDS11 | 6422640 | 6422853 |
| chr_2 | g5009 | g5009.t4 | TSS | g5009.t4 | 6423766 | 6423766 |
Sequences
>g5009.t4 Gene=g5009 Length=1617
ATGAGTGAATCAAATGAAGAACAAAAGTCGATTCCTCCATCTTCAGAGGAATATGCAGCA
TCATTAATTTTGAAATCAAGTAAACCAAGTGGAATTAAGCCTCCATCAACTGCATCATTA
TTCTCATCTGATTCATCAGCACATAGAGTCAGTAGAATTTGTTCAAGTCATCAAAAAAAA
CCAGATCTTCCTACAGCGGCAACACCAAACAAAATATCAGTTGCTTTTGTTGTTAAACAT
GAAAACACCACACTTTCAGGTGAACTCAGTAACAACGACTACGGTGACACAATGCGACGT
CAAAGCGATGATTATAAAACACACTATTTACCAGATGTAAGTGAAGAAAGCGAATATGAC
TTGCTATATGACCGTTTTGGACTTGGTTATCGCTCATCTAAATCTAAATCACAATCACCT
GATCCATTTCGATTGTACAAGTATTCGCCCGATCGCAAAAGTTCAAGTGGTATATCCTCC
TCTGTATCACCAGACTTTTTTGAAGCCACTGGCAGACGATCAAGCTCAGATCATGGAGCA
GATTTAACGACAGACACAGATAGTTTTATGATAGGAAATCGAGTTTATGTTGGAGGAGTT
AAACCCGGTCGTATTACTTTTATTGGCGAAGTTCATTTCGCCCCGGGTGAATGGGCTGGA
GTTGTTTTAGATGAGCCAGAAGGCAAAAATGATGGTGCAGTTAGTGGAAAACGCTATTTT
CAGTGTGAACCTAAAAAGGGAATATTTTCACGCCTCACACGACTAACTCGTGAACCATTA
TCATCAACCACAACTGATGGTCCATTAAGTACAGATTATAGCTTCCGTTCATTTACATCA
CCACTTCGAAACACATCGGGAAATACATCACCAACACAGAGTGTTTCTAGTGTCTCTAAA
ACAGCAGCTGGAACAAAAATTATTCCCGAAATAAATGATCGTGTTATTGTCAAGAGTGCA
ACTGGAAGTCGTGCTGGAATTCTTCGTTATCGTGGAGAGCCAGCATTTGCTAGTGGTATT
TGGTGTGGTGTTGAATATGAAGAGCCTGTTGGCAAAAATGACGGATCAGTTAGTGGACAA
AGATATTTCAAATGCGCACCCAATCATGGAATTTTTGTGCCTGAAGGAAAGGTTGTTTTA
TCACCATTAGCACGAAAAATGCGCCTTTCAAGACAAAATTCACAAGAATCGTTAACATCA
AACATTACACTTAACAGCTTGGCTTCGACAAATACTTCAAAATTGCGGTTAAATGCAACA
CAAAAGCGCCTATCGACACTTAATAAGTCACCATCGGCAACGTCAACACCAAAACCCTCG
TTCTCGTTGCAGGACATTTTACGAGAGAAATCGAATCATATTGAACAAATCATGAAAGAA
CGAGATATTGAACGTGAAGAAATGGCAGCTCAAACAGTTCTTTATCAAAAGAATCTTAAT
CAGACATTGTCTTATTTACAAAAGAGTCCAAGTCCTGACGTTGAAGAACATATTGGAAGA
TGGGCTACATATATTCGACAGAGAAGTGAACACATTGATGACTTGAGACGACAATTCACA
GGTTGGACTGGCAATCACGAGAGACATTGCATTCTTCATGATGTCTTTTTGACATAA
>g5009.t4 Gene=g5009 Length=538
MSESNEEQKSIPPSSEEYAASLILKSSKPSGIKPPSTASLFSSDSSAHRVSRICSSHQKK
PDLPTAATPNKISVAFVVKHENTTLSGELSNNDYGDTMRRQSDDYKTHYLPDVSEESEYD
LLYDRFGLGYRSSKSKSQSPDPFRLYKYSPDRKSSSGISSSVSPDFFEATGRRSSSDHGA
DLTTDTDSFMIGNRVYVGGVKPGRITFIGEVHFAPGEWAGVVLDEPEGKNDGAVSGKRYF
QCEPKKGIFSRLTRLTREPLSSTTTDGPLSTDYSFRSFTSPLRNTSGNTSPTQSVSSVSK
TAAGTKIIPEINDRVIVKSATGSRAGILRYRGEPAFASGIWCGVEYEEPVGKNDGSVSGQ
RYFKCAPNHGIFVPEGKVVLSPLARKMRLSRQNSQESLTSNITLNSLASTNTSKLRLNAT
QKRLSTLNKSPSATSTPKPSFSLQDILREKSNHIEQIMKERDIEREEMAAQTVLYQKNLN
QTLSYLQKSPSPDVEEHIGRWATYIRQRSEHIDDLRRQFTGWTGNHERHCILHDVFLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5009.t4 | Coils | Coil | Coil | 447 | 467 | - |
| 8 | g5009.t4 | Gene3D | G3DSA:2.30.30.190 | - | 173 | 266 | 4.3E-31 |
| 7 | g5009.t4 | Gene3D | G3DSA:2.30.30.190 | - | 285 | 386 | 1.5E-27 |
| 15 | g5009.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 45 | - |
| 14 | g5009.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 30 | 45 | - |
| 3 | g5009.t4 | PANTHER | PTHR18916:SF79 | RESTIN HOMOLOG | 155 | 486 | 4.2E-88 |
| 4 | g5009.t4 | PANTHER | PTHR18916 | DYNACTIN 1-RELATED MICROTUBULE-BINDING | 155 | 486 | 4.2E-88 |
| 1 | g5009.t4 | Pfam | PF01302 | CAP-Gly domain | 191 | 254 | 1.1E-21 |
| 2 | g5009.t4 | Pfam | PF01302 | CAP-Gly domain | 311 | 378 | 3.9E-23 |
| 10 | g5009.t4 | ProSitePatterns | PS00845 | CAP-Gly domain signature. | 209 | 240 | - |
| 11 | g5009.t4 | ProSitePatterns | PS00845 | CAP-Gly domain signature. | 332 | 363 | - |
| 16 | g5009.t4 | ProSiteProfiles | PS50245 | CAP-Gly domain profile. | 209 | 251 | 17.73 |
| 17 | g5009.t4 | ProSiteProfiles | PS50245 | CAP-Gly domain profile. | 332 | 374 | 18.036 |
| 13 | g5009.t4 | SMART | SM01052 | CAP_GLY_2 | 191 | 256 | 1.4E-28 |
| 12 | g5009.t4 | SMART | SM01052 | CAP_GLY_2 | 311 | 379 | 4.4E-31 |
| 5 | g5009.t4 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 172 | 273 | 1.96E-32 |
| 6 | g5009.t4 | SUPERFAMILY | SSF74924 | Cap-Gly domain | 310 | 392 | 4.71E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5009/g5009.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5009.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K10421 (CAP-Gly domain-containing linker protein 1)
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.
