General information for g11880.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative TBC1 domain family member 4.
Parent gene
- The parent gene g11880 is located on chr_1: 18951292..18952488 (- 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_1 | g11880 | g11880.t6 | isoform | g11880.t6 | 18949062 | 18950665 |
| chr_1 | g11880 | g11880.t6 | exon | g11880.t6.exon1 | 18949062 | 18950137 |
| chr_1 | g11880 | g11880.t6 | cds | g11880.t6.CDS1 | 18949064 | 18950137 |
| chr_1 | g11880 | g11880.t6 | exon | g11880.t6.exon2 | 18950333 | 18950665 |
| chr_1 | g11880 | g11880.t6 | cds | g11880.t6.CDS2 | 18950333 | 18950629 |
| chr_1 | g11880 | g11880.t6 | TSS | g11880.t6 | 18950637 | 18950637 |
| chr_1 | g11880 | g11880.t6 | TTS | g11880.t6 | NA | NA |
Sequences
>g11880.t6 Gene=g11880 Length=1409
ATTTCAAATTTGTCGGATCGTATAAAGCAGTCTCAAATGGGACGCTCAATTGAAAACATG
ACTTCGACACATTCAACCATGGAAGAGTCAGTACAAGTTAAAAAAGATCGAATGGCCAAT
TTCAAAAAATCACATATTAGTCACTCAACTGGTGATTTGTATTTAAATAATCGCTCAAAT
TTATCACTTTTTGGAGACTTTCAATTAAATGACTCACAATTTTTTGAAGTCATGTATGTT
GGAAAAATTCGTGTTTCACATAAGAAACTACCGAAAACATTTATTGATGATGCTCTTCCA
AAGTTTATTGCTCACGATAAGATGAAAATAAAGAGTATTGAGGTGAATGGGAAACAAAAT
ACAGACAGTCAACAGACGCCAGAAAATTCTCAAAACGGATATGATAAAAAAATTGACGAG
GAAAGCGATTCATCAAGCGTTAAGAGCAGTGATAGCAAAAGTCAGAGTGATGAAACAAAC
AAACAACAACCAAATTTTCATCGACTTGATTCAATAAAAGCTGAAGAAATACCAAAAAGA
AATCGATCAGCTTCATTTAGTTCAATTGAACAAAATCGTACAATGGTATACATTTTAGGA
AGATCAGATTTGAGATTGATAAGTCCCGATCGAAAACAAATTTTGCTTCATAAAAATTTT
AATGATGTCGTTAATGCTGTTCAAGGAATTAATAGTGCTGAACATTTTGGAATTATTTGC
AATGAAGTGAAAGATAATAAACAAGAATTTATTGGTTATGTCTTTAAATGTCAATCTGCT
GTCATTGCACATGATGTTGTCTCATCTATGTTGAAATCTTTAGAGACACTTGAGCAAGAT
AAAAAATATTCAGATGAAAATTTTGAAGACTCAAAAAAGATGTCAGGTTCTTTACAATGC
GATCATTGTCCTTTAGTATGGTTCAATAAGCTTCAAAATTCAGTTCAAGGTCTCAGCGAA
AAAAAAATTTATAGTGTCATAATGAAACATATTGAAGAATTGAATGCTGACGACTATGAA
ATATTAATGGAAAAATTCTTTGCTTCTGATAAAGTCAATGATTATTCCCTCACAGAACGT
AATAAATTTCTCATGGCACTAATTGAAGCACATTGTCAAATGCGTCAACAGCGACATGTG
CACGATACAATTGAAAATCGATCAGAATTCTTAAATTACTATCTAGGTGGCAGTACAATT
TTAATGAAGGCAAAACGTTCTTTGTCAAGCTCGTTTGATCAACTATTAAAAAGAAGAGGA
AGTAAGGATTCAAATGAAAATAACCACATTACAATTCATGAAGAAGAGCAAAGAAAGTTC
AAACCAATTAGATCAATATCGTTGACATCTCCTTTAATATCACCTTGTGATAATAAACAA
CAATTATTGAATACATCTAAAATGGACAT
>g11880.t6 Gene=g11880 Length=457
MGRSIENMTSTHSTMEESVQVKKDRMANFKKSHISHSTGDLYLNNRSNLSLFGDFQLNDS
QFFEVMYVGKIRVSHKKLPKTFIDDALPKFIAHDKMKIKSIEVNGKQNTDSQQTPENSQN
GYDKKIDEESDSSSVKSSDSKSQSDETNKQQPNFHRLDSIKAEEIPKRNRSASFSSIEQN
RTMVYILGRSDLRLISPDRKQILLHKNFNDVVNAVQGINSAEHFGIICNEVKDNKQEFIG
YVFKCQSAVIAHDVVSSMLKSLETLEQDKKYSDENFEDSKKMSGSLQCDHCPLVWFNKLQ
NSVQGLSEKKIYSVIMKHIEELNADDYEILMEKFFASDKVNDYSLTERNKFLMALIEAHC
QMRQQRHVHDTIENRSEFLNYYLGGSTILMKAKRSLSSSFDQLLKRRGSKDSNENNHITI
HEEEQRKFKPIRSISLTSPLISPCDNKQQLLNTSKMD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11880.t6 | CDD | cd01269 | PTB_TBC1D1_like | 54 | 258 | 1.71038E-49 |
| 11 | g11880.t6 | Gene3D | G3DSA:2.30.29.30 | - | 59 | 272 | 9.9E-6 |
| 7 | g11880.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 103 | 173 | - |
| 9 | g11880.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 103 | 120 | - |
| 8 | g11880.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 121 | 135 | - |
| 10 | g11880.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 136 | 155 | - |
| 2 | g11880.t6 | PANTHER | PTHR11232 | PHOSPHOTYROSINE INTERACTION DOMAIN-CONTAINING FAMILY MEMBER | 59 | 122 | 7.8E-28 |
| 4 | g11880.t6 | PANTHER | PTHR11232:SF67 | - | 59 | 122 | 7.8E-28 |
| 1 | g11880.t6 | PANTHER | PTHR11232 | PHOSPHOTYROSINE INTERACTION DOMAIN-CONTAINING FAMILY MEMBER | 175 | 369 | 7.8E-28 |
| 3 | g11880.t6 | PANTHER | PTHR11232:SF67 | - | 175 | 369 | 7.8E-28 |
| 6 | g11880.t6 | SMART | SM00462 | PTB_9 | 58 | 274 | 2.5E-10 |
| 5 | g11880.t6 | SUPERFAMILY | SSF50729 | PH domain-like | 51 | 257 | 9.57E-13 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed