General information for g12199.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Recombination repair protein 1.
Parent gene
- The parent gene g12199 is located on chr_1: 21696336..21698065 (+ 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 | g12199 | g12199.t1 | TSS | g12199.t1 | 21696223 | 21696223 |
| chr_1 | g12199 | g12199.t1 | isoform | g12199.t1 | 21696336 | 21698065 |
| chr_1 | g12199 | g12199.t1 | exon | g12199.t1.exon1 | 21696336 | 21697307 |
| chr_1 | g12199 | g12199.t1 | cds | g12199.t1.CDS1 | 21696336 | 21697307 |
| chr_1 | g12199 | g12199.t1 | exon | g12199.t1.exon2 | 21697360 | 21697871 |
| chr_1 | g12199 | g12199.t1 | cds | g12199.t1.CDS2 | 21697360 | 21697871 |
| chr_1 | g12199 | g12199.t1 | exon | g12199.t1.exon3 | 21697927 | 21698065 |
| chr_1 | g12199 | g12199.t1 | cds | g12199.t1.CDS3 | 21697927 | 21698065 |
| chr_1 | g12199 | g12199.t1 | TTS | g12199.t1 | 21698174 | 21698174 |
Sequences
>g12199.t1 Gene=g12199 Length=1623
ATGGCAAAAACTAAAGCAGCTTCAAAAAGTCAACCGAAAGCAAAAGATAAAGTAGAAATT
GAGAAAATTCAGGATCAAATAGTTCCAGAATTAGAAAAAGTTGAAGAACCAAAGAAACGA
GCACAAAAAAAGGAAAAAATTGTTTCAAGTAAAACAATTGATAAGGAGCAAAATGAAGAA
CCACAAAAATCTAAAGCTGTAGTTTCTAAGAAGAAAGCTGCAAAATTAACTGAAAAACAG
AATGATGAGAAAATAGATGAAGAAGAGCCACAACAAACCAAAGCTGCTCCTAAGAGAAGA
GCTGCTCAGAAAAAAGTAATAGAAAACGATGAGGATAATGATGAGGAAGCAGAAGAGCCG
AAAACATCTAAAACAAAAAAGACTACTACTAAGAAACCAGCTAAACAAGAAGAACTTGAA
AATAATGAACAAAATTCTGATGAAGTTGAAAGTCCTAAAGAAAAAAAAACTGCTGCTAAA
TCTACAAAAACTAAAGCAGAAAAGAAACCAGCTCAAAAGAAAGTAACTAAAACAACAGAA
AACAATGAAGGCAAAGAAGAGCAATTGGATCAACAAAAGGCCAAAACTGCTCCTAAAAGA
AAAGCTGTTCAGAAGAAGGCTTCTGAAAATGACGAAAAAGATCAGTTAGATGAAGTACAA
AGCCCAAAAAAAGCTAAAGTTACTGCAACAAAAAAGAACACTAAAGCAGCAAAAAAAGAA
CCTGAAAATGATGAAGAAATTTCTGATGAGATTGTAAGTCCAAAGAAGAAAACTGCAAAG
CAAGTAAATGGTAGTGCTGAAAAAAAGAAACTTCTCAATAGCACTGAATCGGACTATAAC
ATTGATTTCAACATTAAAAAGGACTTTGCCACTAAAATTGTCACTTGGAATGTAGCAGGT
GCTCGCAGCTGTTTACAAAAAGGCTTGGTTGAATATTTGAGACGCGAAAATGCTGATATA
ATCTGTTTAAACGAGGTAAAAATTGGATCCGAAAAAGAAATTCCAAAAGAATTGAAAATT
CCTGAATATTATCATTACTTCAATATTGGTAAAGGAAATCCAGGTGTTGCAATTTTTACT
AAGAAGAAGCCTATTAAAGTCACTAATGATTTACCTGAAATATTTACTAACGATAATCGT
TTGATTACTGCTGAATATGAAGATTTTTATCTGGTCTCTTGCTATGTCGTAAATGCAGGT
CAAGGTTTGAAAACTCTTGATAAGCGTTTAGAATGGAATCGAGTCTTTGACAAATACATT
CAAGAACTTGATAAAGAAAAACCTGTCATTATCGCAGGTGATTTGAATGTTAGCCATAAC
GAAATTGATTTGGCAAATCCAAAAAGTAATCAAAGGAGCGCCGGTTTTACAAAGGAAGAG
AGAGATGGTTTTACAAAGTTACTATCTTATGGTTTCATCGATACATTCCGTGAGCTTTAT
CCCAAACAAGAAGGAGCTTACACTTTTTGGTCATATAGATTTAATGCACGTGCTAAAAAT
ACGGGCTGGAGATTGGACTATTTTGTAGTCAGCGAACGGTTTATGGAAAATGTCGTAGAC
AATGTTATTCGTACTAATATTCTTGGGAGCGACCACTGTCCGTTGGTCCTTTTCCTTAAT
TAA
>g12199.t1 Gene=g12199 Length=540
MAKTKAASKSQPKAKDKVEIEKIQDQIVPELEKVEEPKKRAQKKEKIVSSKTIDKEQNEE
PQKSKAVVSKKKAAKLTEKQNDEKIDEEEPQQTKAAPKRRAAQKKVIENDEDNDEEAEEP
KTSKTKKTTTKKPAKQEELENNEQNSDEVESPKEKKTAAKSTKTKAEKKPAQKKVTKTTE
NNEGKEEQLDQQKAKTAPKRKAVQKKASENDEKDQLDEVQSPKKAKVTATKKNTKAAKKE
PENDEEISDEIVSPKKKTAKQVNGSAEKKKLLNSTESDYNIDFNIKKDFATKIVTWNVAG
ARSCLQKGLVEYLRRENADIICLNEVKIGSEKEIPKELKIPEYYHYFNIGKGNPGVAIFT
KKKPIKVTNDLPEIFTNDNRLITAEYEDFYLVSCYVVNAGQGLKTLDKRLEWNRVFDKYI
QELDKEKPVIIAGDLNVSHNEIDLANPKSNQRSAGFTKEERDGFTKLLSYGFIDTFRELY
PKQEGAYTFWSYRFNARAKNTGWRLDYFVVSERFMENVVDNVIRTNILGSDHCPLVLFLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12199.t1 | CDD | cd09087 | Ape1-like_AP-endo | 292 | 539 | 4.98109E-138 |
| 6 | g12199.t1 | Coils | Coil | Coil | 175 | 195 | - |
| 5 | g12199.t1 | Gene3D | G3DSA:3.60.10.10 | - | 249 | 540 | 7.3E-86 |
| 11 | g12199.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 262 | - |
| 9 | g12199.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 110 | - |
| 12 | g12199.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 225 | - |
| 10 | g12199.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 233 | 262 | - |
| 2 | g12199.t1 | PANTHER | PTHR22748 | AP ENDONUCLEASE | 180 | 539 | 1.1E-81 |
| 3 | g12199.t1 | PANTHER | PTHR22748:SF6 | DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE | 180 | 539 | 1.1E-81 |
| 1 | g12199.t1 | Pfam | PF03372 | Endonuclease/Exonuclease/phosphatase family | 294 | 532 | 3.9E-21 |
| 8 | g12199.t1 | ProSitePatterns | PS00728 | AP endonucleases family 1 signature 3. | 500 | 511 | - |
| 15 | g12199.t1 | ProSiteProfiles | PS51435 | AP endonucleases family 1 profile. | 291 | 540 | 43.941 |
| 4 | g12199.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 292 | 539 | 2.62E-67 |
| 13 | g12199.t1 | TIGRFAM | TIGR00195 | exoDNase_III: exodeoxyribonuclease III | 292 | 538 | 5.4E-77 |
| 14 | g12199.t1 | TIGRFAM | TIGR00633 | xth: exodeoxyribonuclease III (xth) | 292 | 539 | 1.9E-84 |
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:0003677 | DNA binding | MF |
| GO:0006281 | DNA repair | BP |
| GO:0004519 | endonuclease activity | MF |
| GO:0004518 | nuclease activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10771 (AP endonuclease 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.
