General information for g12142.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Inactivation-no-after-potential D protein.
Parent gene
- The parent gene g12142 is located on chr_1: 21330838..21334977 (- 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 | g12142 | g12142.t2 | isoform | g12142.t2 | 21308521 | 21311959 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon1 | 21308521 | 21308700 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS1 | 21308521 | 21308700 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon2 | 21308928 | 21309062 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS2 | 21308928 | 21309062 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon3 | 21309130 | 21309288 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS3 | 21309130 | 21309288 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon4 | 21309353 | 21309706 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS4 | 21309353 | 21309706 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon5 | 21310002 | 21310103 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS5 | 21310002 | 21310103 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon6 | 21310169 | 21310286 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS6 | 21310169 | 21310286 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon7 | 21310400 | 21310494 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS7 | 21310400 | 21310494 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon8 | 21310659 | 21310852 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS8 | 21310659 | 21310852 |
| chr_1 | g12142 | g12142.t2 | exon | g12142.t2.exon9 | 21311926 | 21311959 |
| chr_1 | g12142 | g12142.t2 | cds | g12142.t2.CDS9 | 21311926 | 21311959 |
| chr_1 | g12142 | g12142.t2 | TSS | g12142.t2 | NA | NA |
| chr_1 | g12142 | g12142.t2 | TTS | g12142.t2 | NA | NA |
Sequences
>g12142.t2 Gene=g12142 Length=1371
ATGGAAACAATCTCGGAGGAGGAGGAGATTGAAGACAAAATAAAGAAACGTTATGGAAAT
TTGGGAACAGTATTATGTCACACAATCGATAGAGGAAATAGCTCTAGCATTGGAATATCA
TTAGCTGGACATCGTGATCGAAATAAAATGGCATGCTTTATTGCCGGTATCAATCCAAAG
GGAATTGCATCGTCTGGTGGATTAGAAATTGGCGACGAGATTCTTGAGGTTAATGGCATT
GTACTACATGGAAGATGTCATTTGAATGCATCAGCAATAATCAAAGGACTGCCTGGTTCT
GTTATGCAATTTATTGTCCTTAGAAGAAAGCAAGCATTAGAAGACTTAGCTGTTAAGCCT
GTAACTCAATTCCCTGTTGAGATCTCAAACGAGGACGCTTTTGCCACTTTTAAAAATGTT
CGTCATGTAACAATCAAGAAGGGCAATCAGAGCTTAGGTATTATGATTATTGAAGGAAAG
CATGCGGAAGTTGGGCAGGGCATTTTTGTATCAGATATTCAAGAAGGATCTAATGCTGAA
AAGGCCGGCCTTAGTATTGGTGACATGATATTAGCTGTTAACAAAGATTCCCTTCTTGGC
TGTAATTATGAAACGGCAGCGAGTATGCTTAAGAAGACAGAAGGAATCGTGGTGCTTACT
GTATGTAATCCAAATAAAAAAGACAATGAGACAGTTATCAAAAAAGACATAGAGCAGCCG
GAAAAGGGACCAAGTCGTCCACTAACGCCAAAGCCACAGCCTTCACCAGCAAAAGAAGCC
GCATCAGATCCAACGACCTGCGAAATTGCCAATAATCACAACACCGTCATTGAAATAAAA
TTGGAAAATAATCCGATTGGTATTCAAGTTGCTGGTGGTTGTGATACGTTAGTTAATACT
GGAGCTGTAATAGTTAACATATTACCTGGCAGCATTGCCGAAAAAGACAAACGTTTGCAA
GTGTTCGATCAAATACTCGAAATAAATTCGACCAAGATCACGCAAGAGTTGACATGTGAG
CTAATTCAGCGAGCTGTGAAACAAGTGCAATCAAAAGTGAAAATGACGATATATCGTGCC
GATCCACCCGAAGTAGAATCAATGGAAATTGAGTTAACAAAGAAACCTGGCAAGAACCTT
GGAATTGGATTTTTCACTTCAAATCCTCGTGGAATGCTTGTCACAGATATCGTTACCGGA
GGTATAGCCGATCTTGATGGTCGCATTCAAAAAAGTGATATTGTAACACATGTCAATTCG
GAAAAAGTAAGCAATATGAGCGTAGAAGAATGTTCGACACTGTTAAAGGCGATTCAAGGA
AAGGTCACCTTTAAAATATTGCGAGCGAAGCCAAAGAAACGTAGCAGTTAA
>g12142.t2 Gene=g12142 Length=456
METISEEEEIEDKIKKRYGNLGTVLCHTIDRGNSSSIGISLAGHRDRNKMACFIAGINPK
GIASSGGLEIGDEILEVNGIVLHGRCHLNASAIIKGLPGSVMQFIVLRRKQALEDLAVKP
VTQFPVEISNEDAFATFKNVRHVTIKKGNQSLGIMIIEGKHAEVGQGIFVSDIQEGSNAE
KAGLSIGDMILAVNKDSLLGCNYETAASMLKKTEGIVVLTVCNPNKKDNETVIKKDIEQP
EKGPSRPLTPKPQPSPAKEAASDPTTCEIANNHNTVIEIKLENNPIGIQVAGGCDTLVNT
GAVIVNILPGSIAEKDKRLQVFDQILEINSTKITQELTCELIQRAVKQVQSKVKMTIYRA
DPPEVESMEIELTKKPGKNLGIGFFTSNPRGMLVTDIVTGGIADLDGRIQKSDIVTHVNS
EKVSNMSVEECSTLLKAIQGKVTFKILRAKPKKRSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g12142.t2 | CDD | cd00992 | PDZ_signaling | 28 | 101 | 2.12092E-14 |
| 18 | g12142.t2 | CDD | cd00992 | PDZ_signaling | 140 | 222 | 6.3333E-18 |
| 20 | g12142.t2 | CDD | cd00992 | PDZ_signaling | 275 | 357 | 2.57255E-10 |
| 17 | g12142.t2 | CDD | cd00992 | PDZ_signaling | 369 | 447 | 2.14297E-9 |
| 16 | g12142.t2 | Gene3D | G3DSA:2.30.42.10 | - | 7 | 112 | 1.7E-19 |
| 14 | g12142.t2 | Gene3D | G3DSA:2.30.42.10 | - | 125 | 222 | 2.1E-26 |
| 13 | g12142.t2 | Gene3D | G3DSA:2.30.42.10 | - | 257 | 364 | 7.9E-22 |
| 15 | g12142.t2 | Gene3D | G3DSA:2.30.42.10 | - | 365 | 456 | 7.0E-25 |
| 25 | g12142.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 231 | 265 | - |
| 6 | g12142.t2 | PANTHER | PTHR19964 | MULTIPLE PDZ DOMAIN PROTEIN | 2 | 368 | 8.6E-79 |
| 8 | g12142.t2 | PANTHER | PTHR19964:SF79 | INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN | 2 | 368 | 8.6E-79 |
| 5 | g12142.t2 | PANTHER | PTHR19964 | MULTIPLE PDZ DOMAIN PROTEIN | 366 | 451 | 8.6E-79 |
| 7 | g12142.t2 | PANTHER | PTHR19964:SF79 | INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN | 366 | 451 | 8.6E-79 |
| 1 | g12142.t2 | Pfam | PF00595 | PDZ domain | 29 | 101 | 3.2E-10 |
| 3 | g12142.t2 | Pfam | PF00595 | PDZ domain | 143 | 221 | 1.0E-12 |
| 2 | g12142.t2 | Pfam | PF00595 | PDZ domain | 279 | 357 | 2.1E-11 |
| 4 | g12142.t2 | Pfam | PF00595 | PDZ domain | 377 | 447 | 1.2E-9 |
| 28 | g12142.t2 | ProSiteProfiles | PS50106 | PDZ domain profile. | 26 | 109 | 14.717 |
| 29 | g12142.t2 | ProSiteProfiles | PS50106 | PDZ domain profile. | 142 | 225 | 18.275 |
| 27 | g12142.t2 | ProSiteProfiles | PS50106 | PDZ domain profile. | 275 | 361 | 15.662 |
| 26 | g12142.t2 | ProSiteProfiles | PS50106 | PDZ domain profile. | 369 | 450 | 16.144 |
| 23 | g12142.t2 | SMART | SM00228 | pdz_new | 35 | 110 | 9.6E-13 |
| 21 | g12142.t2 | SMART | SM00228 | pdz_new | 150 | 225 | 3.9E-16 |
| 22 | g12142.t2 | SMART | SM00228 | pdz_new | 284 | 361 | 2.0E-13 |
| 24 | g12142.t2 | SMART | SM00228 | pdz_new | 380 | 450 | 1.7E-11 |
| 12 | g12142.t2 | SUPERFAMILY | SSF50156 | PDZ domain-like | 25 | 111 | 3.29E-18 |
| 11 | g12142.t2 | SUPERFAMILY | SSF50156 | PDZ domain-like | 121 | 226 | 2.76E-23 |
| 9 | g12142.t2 | SUPERFAMILY | SSF50156 | PDZ domain-like | 252 | 363 | 4.6E-17 |
| 10 | g12142.t2 | SUPERFAMILY | SSF50156 | PDZ domain-like | 362 | 451 | 5.78E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
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