General information for g12784.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Integrin beta-nu.
Parent gene
- The parent gene g12784 is located on chr_1: 26132113..26133966 (- 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 | g12784 | g12784.t1 | TTS | g12784.t1 | 26126502 | 26126502 |
| chr_1 | g12784 | g12784.t1 | isoform | g12784.t1 | 26126804 | 26133966 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon1 | 26126804 | 26127174 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS1 | 26126804 | 26127174 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon2 | 26128720 | 26129120 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS2 | 26128720 | 26129120 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon3 | 26130980 | 26131171 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS3 | 26130980 | 26131171 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon4 | 26131366 | 26132128 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS4 | 26131366 | 26132128 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon5 | 26132187 | 26132748 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS5 | 26132187 | 26132748 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon6 | 26133762 | 26133832 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS6 | 26133762 | 26133832 |
| chr_1 | g12784 | g12784.t1 | exon | g12784.t1.exon7 | 26133891 | 26133966 |
| chr_1 | g12784 | g12784.t1 | cds | g12784.t1.CDS7 | 26133891 | 26133966 |
| chr_1 | g12784 | g12784.t1 | TSS | g12784.t1 | 26134105 | 26134105 |
Sequences
>g12784.t1 Gene=g12784 Length=2436
ATGAGAAATTATTGGGCATTAGCATTGATTTCTTTATTAATAATTAAAATAGTATTAGTC
AATGCAAACAGCAAGTATTGCGTGAATCAGGATACATGTGATAAATGCTTAAATCAACAT
CCAACATGTGCATGGTGTTCTGATCGTCTCTATGAAATGCGAAGGGCGAGATGCATGACA
GAGAAAGATTTGTTAGAGGCAAATTGTCGAAAAGAGTTCATTCAGATCAACCATTATGAG
CCTATGAGTAATGTCAGAGATGATGACTTGCGTGACTTCAATAAAGATTTTGATTCAGTG
CAGATACGACCACAAAGTGTTCGTATGAAATTGCAGAAAAATCGACAGCAGACGGTTAAA
TTGAAATATAAGCCTGCAAAGAATTATCCACTTGATCTTTATCTTCTCATGGATTTAACT
TGGTCAATGCGTGACGATAAAGAAACTTTAGTAAAAATGGGTGGCAGTTTGAGCACATCA
CTTAAGAATTTGACTGAAAACTTTCGTCTTGGCTTTGGGTCATTTGCTGATAAACCAATT
GCACCTTATATTAATCCTGGCACTGAAGACAATCCATGTAAACTCGTACAAGAAACTTGT
CTACCAACTTATGGCTTCAAGCATAAACTTGCAATGACAGACAACATTCAAGAGTTCATT
ACAAAGGTCAATGGAAGTGAAATTACTGGAAATTTGGATAATTTAGAAGGCGGTCTTGAT
GCACTCATGCAAGTGCTAGTATGTAGAGAAGAAATTGGTTGGAATGATAAAACAAGAAAA
ATTGTCGTATTTGCAACTGATGGACCAATGCATTTTGCTGGTGATGGTTTGCTTGCCGGA
TTGGTAAAAAAGAATGATAAAAGCTGTCATTTGAGTGATAAAGGAGAATATATGGCTTCA
TTGGAGTACGATTATCCTTCACTTGAAGAAATTTATCGTGAATTACTCCGAACGAAAGTT
AGTGTCATTTTTGCTGTCACATCTGATGTCATTTATCACTATGATCAAATGCATGAGATT
ATGGAAGAGATTACAAGTGTAGGCCAACTTGCAGCTGATTCTTCTAACATTTTACAGCTT
GTTGAGCAAGGTTTTAAACAAGCAGTTAAAAGAGCACAATTTCAAGATGATGCACCAGAT
TATTTGAGGGTTGAATATAAAACCAATTGTGGTGGAAAATATGAAACTTTACAAGACACA
AACAAGTGTGATAATATTGAAATTGGTAAAGAATATGAATTTGATGTTGGAATTACTTTA
TTAAAATATCCAGATGATGGTGCAAAGAGTGTCAAAATAAAAATTGAAGAAGCAAATATC
GACGCTGAAGCAACAGAAATTGACATTGAAATTGATTATCCATGCACTAATTGTTTGGCA
CATCCTGGTGAAATTGCATCAGCATTGTGCAGTCGAAATGGCGAATACAAATGTGGAGCA
TGCATTTGTGACAGTGGTTATGTTGGTAAACAGTGTGAATGCAATTTACAAGAATATTCA
AGCAGCAAGGAACTTGATAATCAATGTCGTGAGCCAAAAATAACTAATAATAACGAGACA
AAACTTATGCCACCATGCTCGGATCGTGGTGAATGCCTCTGTGGAGAATGTTTCTGTAAT
GCAAATTACGAGGGAAAATATTGTGAATGTGAAACCTGTCCAGTGTCAGATGACAATGGT
GAGGAATGTAATGGTCATGCATTATTTTGTGATTGCGGTGTTTGTCAGTGTCAACCAGAA
TTTACTGGACCAACATGTGAATGTTCAACATTGCAGACCAATTGCATTAGTCCAGATAGC
AAAATGTCAAATGATGGTGGAAAAATCTGTTCAGGGCATGGAACGTGCAAATGCAATCAA
TGCGAGTGTGAAGATTCGCGTACTGGAAAATTCTGTGAAAGCACACCCGGGAATGAGACA
TTTAATTCATTGTGTATATTCTATGAAACGTGCGTACAATGTGTCATAAACCGTAAACTG
CAACACGAGTGCTCGGATTATGAGCAAAAATGTTCCTCGCAGAATGGTTTGCTGTATAAA
TCAGAATTTTATGACAAAATCTCAGATGCAGATATTTTATGTATAGCGCGTGTGAGATAT
GATGATGACACAGTTTGCGAATATAAATTTACGTATGAATTGGATGAAAAATCAGAGACA
AATCTTCGTATTGAGAACACAGATTGTCCGCCAGTGAATGTTGCTGCATATTCAATTATT
GGCATAATCGTTGCGACATTTCTCATTGGATTTCTCATTTTGATGGTAATCAAGTGCAAC
ATGTATATCGCGGAAAAGCGAGAATTTGCTGCATTTGAAAAAGAACGAGATCAACAAACC
GAATATAAGTATGAAAGTCCACTATATAAATCACCAGTGACAACATTCCGTAATCCACAA
TCTACATCACAATCGAATGCTTTCGAAATGAAATAA
>g12784.t1 Gene=g12784 Length=811
MRNYWALALISLLIIKIVLVNANSKYCVNQDTCDKCLNQHPTCAWCSDRLYEMRRARCMT
EKDLLEANCRKEFIQINHYEPMSNVRDDDLRDFNKDFDSVQIRPQSVRMKLQKNRQQTVK
LKYKPAKNYPLDLYLLMDLTWSMRDDKETLVKMGGSLSTSLKNLTENFRLGFGSFADKPI
APYINPGTEDNPCKLVQETCLPTYGFKHKLAMTDNIQEFITKVNGSEITGNLDNLEGGLD
ALMQVLVCREEIGWNDKTRKIVVFATDGPMHFAGDGLLAGLVKKNDKSCHLSDKGEYMAS
LEYDYPSLEEIYRELLRTKVSVIFAVTSDVIYHYDQMHEIMEEITSVGQLAADSSNILQL
VEQGFKQAVKRAQFQDDAPDYLRVEYKTNCGGKYETLQDTNKCDNIEIGKEYEFDVGITL
LKYPDDGAKSVKIKIEEANIDAEATEIDIEIDYPCTNCLAHPGEIASALCSRNGEYKCGA
CICDSGYVGKQCECNLQEYSSSKELDNQCREPKITNNNETKLMPPCSDRGECLCGECFCN
ANYEGKYCECETCPVSDDNGEECNGHALFCDCGVCQCQPEFTGPTCECSTLQTNCISPDS
KMSNDGGKICSGHGTCKCNQCECEDSRTGKFCESTPGNETFNSLCIFYETCVQCVINRKL
QHECSDYEQKCSSQNGLLYKSEFYDKISDADILCIARVRYDDDTVCEYKFTYELDEKSET
NLRIENTDCPPVNVAAYSIIGIIVATFLIGFLILMVIKCNMYIAEKREFAAFEKERDQQT
EYKYESPLYKSPVTTFRNPQSTSQSNAFEMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 43 | g12784.t1 | CDD | cd00198 | vWFA | 131 | 268 | 7.83254E-4 |
| 33 | g12784.t1 | Gene3D | G3DSA:3.30.1680.10 | - | 23 | 77 | 7.4E-11 |
| 28 | g12784.t1 | Gene3D | G3DSA:2.60.40.1510 | ntegrin | 99 | 486 | 4.9E-135 |
| 32 | g12784.t1 | Gene3D | G3DSA:3.40.50.410 | - | 126 | 372 | 4.9E-135 |
| 30 | g12784.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 500 | 552 | 9.6E-10 |
| 29 | g12784.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 553 | 591 | 2.2E-6 |
| 31 | g12784.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 599 | 659 | 2.7E-8 |
| 34 | g12784.t1 | Gene3D | G3DSA:1.20.5.100 | - | 728 | 802 | 7.4E-16 |
| 7 | g12784.t1 | PANTHER | PTHR10082:SF59 | INTEGRIN BETA-NU | 12 | 803 | 9.1E-275 |
| 8 | g12784.t1 | PANTHER | PTHR10082 | INTEGRIN BETA SUBUNIT | 12 | 803 | 9.1E-275 |
| 42 | g12784.t1 | PIRSF | PIRSF002512 | Integrin_B | 1 | 805 | 4.4E-214 |
| 22 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 30 | 46 | 4.9E-79 |
| 16 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 58 | 77 | 4.9E-79 |
| 18 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 101 | 114 | 4.9E-79 |
| 10 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 129 | 147 | 4.9E-79 |
| 14 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 169 | 188 | 4.9E-79 |
| 20 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 200 | 219 | 4.9E-79 |
| 15 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 233 | 255 | 4.9E-79 |
| 9 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 260 | 275 | 4.9E-79 |
| 21 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 304 | 327 | 4.9E-79 |
| 19 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 341 | 365 | 4.9E-79 |
| 11 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 526 | 539 | 4.9E-79 |
| 12 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 733 | 750 | 4.9E-79 |
| 13 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 750 | 768 | 4.9E-79 |
| 17 | g12784.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 785 | 795 | 4.9E-79 |
| 1 | g12784.t1 | Pfam | PF17205 | Integrin plexin domain | 27 | 69 | 8.1E-11 |
| 4 | g12784.t1 | Pfam | PF00362 | Integrin beta chain VWA domain | 126 | 369 | 6.5E-92 |
| 6 | g12784.t1 | Pfam | PF18372 | Integrin beta epidermal growth factor like domain 1 | 463 | 487 | 2.5E-6 |
| 2 | g12784.t1 | Pfam | PF07974 | EGF-like domain | 525 | 548 | 1.2E-5 |
| 3 | g12784.t1 | Pfam | PF07974 | EGF-like domain | 605 | 632 | 2.0E-5 |
| 5 | g12784.t1 | Pfam | PF08725 | Integrin beta cytoplasmic domain | 758 | 799 | 8.9E-9 |
| 37 | g12784.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 38 | g12784.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 39 | g12784.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 41 | g12784.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 22 | - |
| 36 | g12784.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 733 | - |
| 40 | g12784.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 734 | 757 | - |
| 35 | g12784.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 758 | 811 | - |
| 48 | g12784.t1 | ProSitePatterns | PS00243 | Integrins beta chain cysteine-rich domain signature. | 610 | 623 | - |
| 45 | g12784.t1 | SMART | SM00187 | INB_2 | 32 | 458 | 1.7E-161 |
| 47 | g12784.t1 | SMART | SM00327 | VWA_4 | 130 | 365 | 0.0016 |
| 46 | g12784.t1 | SMART | SM01241 | Integrin_b_cyt_2 | 758 | 804 | 6.5E-8 |
| 23 | g12784.t1 | SUPERFAMILY | SSF103575 | Plexin repeat | 23 | 74 | 4.87E-11 |
| 25 | g12784.t1 | SUPERFAMILY | SSF53300 | vWA-like | 126 | 367 | 5.75E-66 |
| 24 | g12784.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 604 | 636 | 6.98E-6 |
| 27 | g12784.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 26 | g12784.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 22 | - |
| 44 | g12784.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 735 | 757 | - |
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 transcript has been annotated with K05719 (integrin beta 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. There were no conditions that were differentially expressed