Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase subunit gamma-1, mitochondrial.

Parent gene

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 g10316 g10316.t1 isoform g10316.t1 8898873 8902361
chr_1 g10316 g10316.t1 exon g10316.t1.exon1 8898873 8901797
chr_1 g10316 g10316.t1 cds g10316.t1.CDS1 8898873 8901797
chr_1 g10316 g10316.t1 exon g10316.t1.exon2 8901860 8902055
chr_1 g10316 g10316.t1 cds g10316.t1.CDS2 8901860 8902055
chr_1 g10316 g10316.t1 exon g10316.t1.exon3 8902111 8902361
chr_1 g10316 g10316.t1 cds g10316.t1.CDS3 8902111 8902361
chr_1 g10316 g10316.t1 TSS g10316.t1 8902374 8902374
chr_1 g10316 g10316.t1 TTS g10316.t1 NA NA

Sequences

>g10316.t1 Gene=g10316 Length=3372
ATGTTGAGACGAGTCGTTAGAAATTATTCATCTTATCTCAATGATTTTGAGCCTTATAGT
GTAGTTAAAATAATTCCTGGAACTAATAAAAACATACAAAATTCAAAGATTCTCGAGAAA
ACAAGTGTTAAAGATGAAAAAGAAGCGGAAAACTGTAATGAAGTTGGTATACAAATGATT
AGTGAAAAATTAAGACAACAAATTTTTGGGAATTCAGAAAAACCAATGTTTCAAGCAGAA
ATCGTTGAAAAATATAGACGAGAGTTGTATGATAATGGTATAAAAGATTTAAAAACCTCC
GAACTTCCAGAAGTTGATTTAAAACTACCAAAGTTAAATGGAAAGAACATTGAAGAGCAT
TTTTATAATATTGCACTCAATCAAGTTGAGAAATATCAAAAACTTGTAAAAACTTTATTA
AATTCACGTTTACCGAAATTACCTGAAAAATGGAATTTTCAAGCAGGATGGACTTGCTAT
GACAGTGAAACTGGATTGTGCTATTCTGTGCCTTTTCCTGAAGAAGATATATTAGTTTTT
GATGTTGAAGTTTGCGTATCAGTTGGAAATTTTCCTGTAATTGCAACTGCTGTTGGTTCA
AAAAACTGGTATTCTTGGACTAGTAAAAAGTTAATTAATATACCTAGAAATGACATAAAA
TCAATGAAAGTAACACCAGATGACCTTATACCAATTGAGTCTACAAATGACGATTTAGGA
TTTGATTTGACAGAGAAACATAAGAAGCCTCGCCTTATAATTGGTCATAATGTTTCTTAT
GATAGAGCAAGGATAAAAGAACAATATTGGATTGAAAATACTGCAACTCGATTTTTAGAT
ACGATGTCATTGCATGTTTGTGTAAGTGGTGTAACAAGTTATCAACGAGCGATGATGAAA
GCACATAAAGATTTATCTGAAGAAGATCAAAATTGGGGAAGTTTAACATCACTCAATAGT
TTAAAAGAAGTACATAAACTTTACTGTAAAAAGAAAGACGAGTTAGACAAAGAAATTAGA
AGTATATTTATGGAAGGAACTCTTAAAGATGTTCGAAATGATTTTCAAAATTTAATGACT
TATTGTGCCAAAGATGTAATTGCAACTAACGAAATCATAAAAGAACTTTATCCTTTATTT
GAAGAAAGGTTTCCTCATCCAGTAACATTGGCTGGAATGTTAGAGTTGAGCTTAGCTTAT
CTACCAATTAACAGTAATTGGTTGAGATATATAAATGAAGCAAATTTAACTTATGAAGAT
TTAGATATCGAATCTAAAACTTTACTTGCACAAAGAGCTGACCATGCATGTCGTTTGAAA
CATCATGATGCTTATAAAAATAATTTATGGATGTGGAGCGAAGATTGGAGTGAACAAGAA
TTACAAATGAAAAAGGGAAAATTAAAAGCTTCTCAGAATTCAACAGAAAATAATGAAAAT
CTTTCAACAAATCAGGAATTGCAAAAATTAAGTAAAACATTTAAACCTTTATATGATAAA
ATGTATTTTCTTCCTGCTCGTCGTCCACTCTTACCTGGTTATCCCTTATGGTACAGAAAT
TTATGTGAAAAATATAATGATTCAGGCAATTGGACACCAGGAGTAATGAATATTGGTACG
GGAATGCAAATTGCACCAAAACTTCTTTCACTTTGTTGGGAAGGATATCCATTGCATTTT
ATTAGAGGTGAAGGTTGGGGTTTTTTGATGCCAACTAAAAAGAAGCGTCCAAACAATGAA
AATGGTGCTATACCATTAGAAACATTGTTAGAAAAATGCCCCTTACAATGTGATCATTTT
GAAGCTAAAGAGGGTGAAACTAATGAAGCTTTAACCACTTTATGGAAAGATGTTGAACAA
AATATTAGTAAAAAGAGCTATTACAATAAAAAGAGTAAAAAGTATTTAGCAGCAAATGTT
GACGATTTATACAAAGGTTCAGGTGTGTGGTGTAATATCGAACTCGAAAATTGTTGTTGG
TTCTTCAAATTACCACATAAAGATGGAAAATCGAAAAATGTTGGTAATCCTCTTGCAAAA
GATTTTATTAATAAATTTTCTGAAAATGTTTTAACTGGTGAGGGACATATTGCTGAGCGA
ATTATTGAAATTGCACGCATGCTTTCTTATTGGCGTAACAATCGTGATCGTATAATGGGT
CAAATGGTTGTATGGCTTCATACACTACCAAAAAATTTATCTTCGAGTGAAATGGAATAT
GGAGCAATTATACCTCAAGTTGTAGTTTGTGGTACATTAACACGTCGTGCAATGGAACCA
ACATGGATGACAGCGAGCAATTCTAAAATTGAAAGAGTAGGATCAGAGCTTCGTGGCATG
GTTCAAGCACCCGAAGGATATAAGATAGTAGGTGCTGATGTTGATTCACAAGAATTATGG
ATAGCTTCTTTATTGGGTGATTCAGAGAGAAAAATTCATGGCTCTACACCATTTGGTTGG
ATGACTTTAAGTGGAACAAAATCAAAAGGAACAGATTTGCATACAATAACAGCAAATGCT
GTTGGTATTTCTCGAGATCATGCAAAAGTAATTAATTATGCTAGAATTTATGGCGCTGGT
CAAAATTTCGCTCAAACTCTACTTAAACAATTTAATCCTTCAATATCAGATAATGAAGCA
AAATCGAAAGCAATAAAAATGTTTGCACTGACAAAAGGAAAGAAAACGTACTATCCTCTG
CCTGAATATCAAGACGAATATCCTACACGAAAAGGCTTCTCAACCTATGAGGCAATGCGT
ATTGCTTCATTAAATGGTAAAAGTGTACTCGAAATGTTTTCAAAAGCACAATGGAATGGC
GGAAGTGAGAGTGCTATGTTTAACAAATTAGAAGAAATTGCCGAAAGCGAATATCCTGTA
ACACCATTTCTTCACTGCAGATTAAGTCGAGCACTTGAACCGCAAACTGGAATTGAAGAT
AGATTTTTGCCAACAAGAATCAATTGGGTTGTTCAAAGCGGTGCAGTAGATTTTCTTCAT
CTTATGCTGGTTACCATGCGATGGTTAATGGGCGAAAAAATAAGATTCTGTCTTAGTTTT
CATGATGAAATTCGATATATTGTTAAGGATGAATATGCAAATCAAGCTGCTTTAGCAATG
CATATAACTAATTTATTAACAAGATCATTTTGTGCCTCTCGGCTTGGATTTCATAGTCTT
CCACAATCAATTGCATTCTTTACATCAGTAGAAATTGATAAAATATTACGTAAAGAAGCT
GAAAATGATTGCAAAACACCATCCAATGAACATGGATTTTCTGGCGGATATTTAATAAAA
CCAGGTGAAGCAATTGATATCTATGAAGCTGTAAAGCGAGTAGGAAATGATATTTCTTCA
TGGACAAAGTAA

>g10316.t1 Gene=g10316 Length=1123
MLRRVVRNYSSYLNDFEPYSVVKIIPGTNKNIQNSKILEKTSVKDEKEAENCNEVGIQMI
SEKLRQQIFGNSEKPMFQAEIVEKYRRELYDNGIKDLKTSELPEVDLKLPKLNGKNIEEH
FYNIALNQVEKYQKLVKTLLNSRLPKLPEKWNFQAGWTCYDSETGLCYSVPFPEEDILVF
DVEVCVSVGNFPVIATAVGSKNWYSWTSKKLINIPRNDIKSMKVTPDDLIPIESTNDDLG
FDLTEKHKKPRLIIGHNVSYDRARIKEQYWIENTATRFLDTMSLHVCVSGVTSYQRAMMK
AHKDLSEEDQNWGSLTSLNSLKEVHKLYCKKKDELDKEIRSIFMEGTLKDVRNDFQNLMT
YCAKDVIATNEIIKELYPLFEERFPHPVTLAGMLELSLAYLPINSNWLRYINEANLTYED
LDIESKTLLAQRADHACRLKHHDAYKNNLWMWSEDWSEQELQMKKGKLKASQNSTENNEN
LSTNQELQKLSKTFKPLYDKMYFLPARRPLLPGYPLWYRNLCEKYNDSGNWTPGVMNIGT
GMQIAPKLLSLCWEGYPLHFIRGEGWGFLMPTKKKRPNNENGAIPLETLLEKCPLQCDHF
EAKEGETNEALTTLWKDVEQNISKKSYYNKKSKKYLAANVDDLYKGSGVWCNIELENCCW
FFKLPHKDGKSKNVGNPLAKDFINKFSENVLTGEGHIAERIIEIARMLSYWRNNRDRIMG
QMVVWLHTLPKNLSSSEMEYGAIIPQVVVCGTLTRRAMEPTWMTASNSKIERVGSELRGM
VQAPEGYKIVGADVDSQELWIASLLGDSERKIHGSTPFGWMTLSGTKSKGTDLHTITANA
VGISRDHAKVINYARIYGAGQNFAQTLLKQFNPSISDNEAKSKAIKMFALTKGKKTYYPL
PEYQDEYPTRKGFSTYEAMRIASLNGKSVLEMFSKAQWNGGSESAMFNKLEEIAESEYPV
TPFLHCRLSRALEPQTGIEDRFLPTRINWVVQSGAVDFLHLMLVTMRWLMGEKIRFCLSF
HDEIRYIVKDEYANQAALAMHITNLLTRSFCASRLGFHSLPQSIAFFTSVEIDKILRKEA
ENDCKTPSNEHGFSGGYLIKPGEAIDIYEAVKRVGNDISSWTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g10316.t1 Gene3D G3DSA:3.30.420.390 - 116 312 2.1E-71
16 g10316.t1 Gene3D G3DSA:3.30.420.390 - 313 403 1.9E-28
3 g10316.t1 PANTHER PTHR10267 DNA POLYMERASE SUBUNIT GAMMA-1 35 1114 0.0
10 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 109 121 2.5E-62
9 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 255 269 2.5E-62
11 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 378 387 2.5E-62
6 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 751 777 2.5E-62
8 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 852 860 2.5E-62
5 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 938 951 2.5E-62
4 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 985 1001 2.5E-62
12 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 1035 1050 2.5E-62
7 g10316.t1 PRINTS PR00867 DNA-polymerase gamma (family A) signature 1051 1067 2.5E-62
1 g10316.t1 Pfam PF18136 DNA mitochondrial polymerase exonuclease domain 103 380 1.9E-97
2 g10316.t1 Pfam PF00476 DNA polymerase family A 676 1068 3.1E-46
18 g10316.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 988 -
19 g10316.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 989 1010 -
17 g10316.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1011 1123 -
20 g10316.t1 ProSitePatterns PS00447 DNA polymerase family A signature. 845 864 -
21 g10316.t1 SMART SM00482 polaultra3 774 1032 2.7E-78
14 g10316.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 75 383 3.84E-14
13 g10316.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 661 1078 1.33E-60

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:0003887 DNA-directed DNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0006260 DNA replication BP
GO:0005760 gamma DNA polymerase complex CC

KEGG

Orthology

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.

Raw TPM values