Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA ligase 4.

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_3 g2448 g2448.t1 isoform g2448.t1 18019599 18023081
chr_3 g2448 g2448.t1 exon g2448.t1.exon1 18019599 18019906
chr_3 g2448 g2448.t1 cds g2448.t1.CDS1 18019599 18019906
chr_3 g2448 g2448.t1 exon g2448.t1.exon2 18020338 18020454
chr_3 g2448 g2448.t1 cds g2448.t1.CDS2 18020338 18020454
chr_3 g2448 g2448.t1 exon g2448.t1.exon3 18020513 18022517
chr_3 g2448 g2448.t1 cds g2448.t1.CDS3 18020513 18022517
chr_3 g2448 g2448.t1 exon g2448.t1.exon4 18022581 18023081
chr_3 g2448 g2448.t1 cds g2448.t1.CDS4 18022581 18023081
chr_3 g2448 g2448.t1 TTS g2448.t1 18023099 18023099
chr_3 g2448 g2448.t1 TSS g2448.t1 NA NA

Sequences

>g2448.t1 Gene=g2448 Length=2931
ATGACTGGCCGTGGCAAAGGAGGCAAAGGTTTAGGAAAAGGAGGTGCAAAGCGTCATCGT
AAAGTTCTTCGTGATAACATTCAAGGTATCACAAAGCCAGCTATTCGTCGTTTAGCTCGT
CGTGGTGGTGTCAAGCGTATTTCAGGCTTGATCTACGAAGAAACTCGTGGTGTCTTGAAA
GTATTCTTGGAAAATGTCATTCGTGATGCAGTCACATACACTGAACACGCAAAGCGCAAG
ACAGTCACAGCTATGGATGTTGTTTATGCTTTGAAACGTCAAGGACGTACTCTCTATGGT
TTCGAGAGTCCAGAAATATTACTTGTCATCATGTCTTTCATGCAGAAATTAGGTTTTATT
GAATTAGTAAATGTTTTTGAGAAGTGCATGAATGCTACAAGTGTTGTTCAACGTGACAAT
TACATGAAAAAATATTTTGAACAAGTTTTTAAATTACAAAAAAGATATTTGAGTGAATCT
CCTAATGGTAACTCAAGTGTGTATCCTTTACTGCGGCTTATTCTTTCAACTGATGAGCAT
GAACGTGCTTACGGATTACAGGAAATAAGATTACGTCAGCTCTTAATTAAAACTTTAGCA
GTTACAGGAGATAATGCAAAGAAAATAGAGGAATGCAATGAAGACGATATTGGTGAGAAG
GTTTGTGAGATAATCGGTTCAAATAAAATATCAAAATTGTCAATAGCAGACGTAGATGAT
GCACTTAATCAAATTTCAAATAATCAAAAAATTAACGAACAAAAATTGCAACTTGAAAAG
CTTTATTTAAAAGGATCTGGTAAATGTCTCAAATGGATCGTCAAGATAATTCTTAAAAAC
ATGAAACTCAAAATATCACCTGCAAAGATTCTAGAGAAAGTTCATCCGCTTGGAGGAAAA
CTTTTTACCAAATACAATCATCTTTCAACTGTGATAGAATTTATTGAAAAAGGACAAGCG
ATTGAAGCAATGAAAGATGTTATTAAGCCTTTTACACCGATCAGAGCTATGCTATCGCAA
AAATTTTCTATAGACATGAACAAGATGTTAGAGAAATTTGAACTATATCAAGAGATAAAA
ATGGATGGTGAACGATTTCAGTTGCATATGGAAAATGGAGAATACAAATATTTTTCACGT
AATGCACACGATTTTAGTCAATGTTTTAATCAGTTCATAACTCCATTAATTAAATACAAA
GTAGTAGTGCATAGTGTGATTCTCGATGGTGAAATGATTATTTGGAATAAAGAATTGAGA
CGATTTGTTACAAAAGGAGAGACTGATATGGATGTAAAAAAGATGAAAGATATCAATCAT
AATATGCGACCATGCTTTTGTGCCTTTGATGTGCTTTATTTAAATGGAACAAGTTTTATC
GATCAGCCATTTTATCGTCGTTATGAAATTCTTCATTCACTTTTTGATGATCGTGTTGGA
GTGTTGATAAAAACAAATCCAGTTAAAATAAGAGATGTTGAACATTTAGTATCACAATTC
AACAAAGCATTAGATAACAATGAGGAAGGTATCATTCTAAAGAAAGCAGATTCAACCTAC
ATGCCAGGAGAACGAGATAAAGGAGGATGGTACAAAATGAAAGCTGATTATTTCAATGAT
GAAGTTGTGGAAGATTTTGATTGCGTCATCATTGGTGGATATTTTAAAAATCCTCATACA
CGTGATTTAATTCAAACATATCTGATGGGAATAATTGAGAAGCAATCAGATGGATCCTTT
AATGTATATTCTGTTGGTGATGTTGCTACAGGAATTAAAGATATTGAACGAAAAAACTTA
CATGATAAACTTATGCCAAATACAGTTAACTATTGTGGAGGGACAATCATTGACTTTGAG
AAAGGTAAAATTTTTCTTGGTCAAAATAAAAATAAACCAGATGTCATCATTTTACCTCAC
AAGTCAATTGTTTTGCAAGTTCGTGTATCTGAATTAGCTCCATCAAGTGATTTTTTCACT
GAATACTCATTTAGATTTCCAAGAATTGATTCTATTAGATTTGATAAATGTTGGGATGAA
TCTTGTACTATGCAGCAATTTCAACAAATGTGTAAGACTGGAAATAAAGTTGATGGACGA
GTGGTTAAAGTTAATAAACGAAATGTTGATGCTAAAGATATTCTTTCACCCGAGAAGAAA
CGTCGCATTGCATTTGGAAAATCACGAGTAAGAGCAATCGAAAATTTTTGTCACGATTCA
CAAGAAGATGTTGAACCAATTGATGATGTACTAAATGGGATGGAATTTTGTGTTAAAACA
ACTTCTAAAAATTTACCATCAATAAATGATTTAAAATTACTTCTTAAAATACACGGCGCA
TCATTGACTGAATTTCCCCGAAAGAAGAAAACTTTTGCAGTCATTGCTGGTGACATTGAA
CAACAAATTAAAATTTATATAAATGACAAGGATATTCCAAGACTCACGCCATTAGATTTT
CATTTTATGACCGATGAAATGTACGAAGAAAAATTTAGGAAAGAGTATGACAAATATGGT
GATTCTTATCATGAGGTTCTTGAGACAGTTGATGAAATGATGAAAATAGTTAATAATATG
CAGATTGAATTTGATATTTGTTCTCAAGAAATAAAAGAGCTACGACAAGAAATTTTTGAT
TTTAGTGGAACTGAAAATTTTAAAATCTTTCAAGGGTACTATGCAAAATTTATCTATGGA
GATGAGTTCAACATGACTATGAAGTGGAGTGAAAAAATCTTTGAGTTCTTAGGAGGTGTA
ATTATCAACAAACAAAATAGAAGGGATTTGTTAATTTTCGTCGATAAGGAAACATTTAAT
ATTCGAATACATCCAGAACTGAAAAACTTTCAAATTATTGATTATAAATTTATACTAAAA
TCTAATGATAATAACGCACTTGAAATATTAAACGATTACATGATAAAATAA

>g2448.t1 Gene=g2448 Length=976
MTGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFESPEILLVIMSFMQKLGFI
ELVNVFEKCMNATSVVQRDNYMKKYFEQVFKLQKRYLSESPNGNSSVYPLLRLILSTDEH
ERAYGLQEIRLRQLLIKTLAVTGDNAKKIEECNEDDIGEKVCEIIGSNKISKLSIADVDD
ALNQISNNQKINEQKLQLEKLYLKGSGKCLKWIVKIILKNMKLKISPAKILEKVHPLGGK
LFTKYNHLSTVIEFIEKGQAIEAMKDVIKPFTPIRAMLSQKFSIDMNKMLEKFELYQEIK
MDGERFQLHMENGEYKYFSRNAHDFSQCFNQFITPLIKYKVVVHSVILDGEMIIWNKELR
RFVTKGETDMDVKKMKDINHNMRPCFCAFDVLYLNGTSFIDQPFYRRYEILHSLFDDRVG
VLIKTNPVKIRDVEHLVSQFNKALDNNEEGIILKKADSTYMPGERDKGGWYKMKADYFND
EVVEDFDCVIIGGYFKNPHTRDLIQTYLMGIIEKQSDGSFNVYSVGDVATGIKDIERKNL
HDKLMPNTVNYCGGTIIDFEKGKIFLGQNKNKPDVIILPHKSIVLQVRVSELAPSSDFFT
EYSFRFPRIDSIRFDKCWDESCTMQQFQQMCKTGNKVDGRVVKVNKRNVDAKDILSPEKK
RRIAFGKSRVRAIENFCHDSQEDVEPIDDVLNGMEFCVKTTSKNLPSINDLKLLLKIHGA
SLTEFPRKKKTFAVIAGDIEQQIKIYINDKDIPRLTPLDFHFMTDEMYEEKFRKEYDKYG
DSYHEVLETVDEMMKIVNNMQIEFDICSQEIKELRQEIFDFSGTENFKIFQGYYAKFIYG
DEFNMTMKWSEKIFEFLGGVIINKQNRRDLLIFVDKETFNIRIHPELKNFQIIDYKFILK
SNDNNALEILNDYMIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g2448.t1 CDD cd00076 H4 18 101 1.15334E-50
21 g2448.t1 CDD cd07903 Adenylation_DNA_ligase_IV 325 539 5.2041E-69
20 g2448.t1 Coils Coil Coil 857 877 -
18 g2448.t1 Gene3D G3DSA:1.10.20.10 Histone 2 103 1.1E-57
17 g2448.t1 Gene3D G3DSA:1.10.3260.10 - 110 321 1.6E-34
16 g2448.t1 Gene3D G3DSA:3.30.470.30 DNA ligase/mRNA capping enzyme 329 536 1.4E-52
19 g2448.t1 Gene3D G3DSA:2.40.50.140 - 538 695 1.0E-29
5 g2448.t1 PANTHER PTHR45997:SF1 DNA LIGASE 4 115 899 1.5E-135
6 g2448.t1 PANTHER PTHR45997 DNA LIGASE 4 115 899 1.5E-135
7 g2448.t1 PRINTS PR00623 Histone H4 signature 5 16 5.8E-59
10 g2448.t1 PRINTS PR00623 Histone H4 signature 20 39 5.8E-59
8 g2448.t1 PRINTS PR00623 Histone H4 signature 40 60 5.8E-59
12 g2448.t1 PRINTS PR00623 Histone H4 signature 62 76 5.8E-59
9 g2448.t1 PRINTS PR00623 Histone H4 signature 77 89 5.8E-59
11 g2448.t1 PRINTS PR00623 Histone H4 signature 89 100 5.8E-59
1 g2448.t1 Pfam PF15511 Centromere kinetochore component CENP-T histone fold 40 96 1.3E-6
2 g2448.t1 Pfam PF04675 DNA ligase N terminus 119 295 4.9E-21
4 g2448.t1 Pfam PF01068 ATP dependent DNA ligase domain 337 534 6.9E-44
3 g2448.t1 Pfam PF04679 ATP dependent DNA ligase C terminal region 561 676 4.7E-8
25 g2448.t1 ProSitePatterns PS00047 Histone H4 signature. 15 19 -
27 g2448.t1 ProSiteProfiles PS50160 ATP-dependent DNA ligase family profile. 437 573 25.005
24 g2448.t1 SMART SM00417 h44 16 90 2.9E-29
23 g2448.t1 SMART SM00803 TAF_cls 28 93 0.0086
13 g2448.t1 SUPERFAMILY SSF47113 Histone-fold 3 102 1.53E-30
15 g2448.t1 SUPERFAMILY SSF56091 DNA ligase/mRNA capping enzyme, catalytic domain 330 535 1.44E-40
14 g2448.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 543 692 9.42E-20
26 g2448.t1 TIGRFAM TIGR00574 dnl1: DNA ligase I, ATP-dependent (dnl1) 184 691 6.4E-78

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:0005524 ATP binding MF
GO:0003910 DNA ligase (ATP) activity MF
GO:0046982 protein heterodimerization activity MF
GO:0006352 DNA-templated transcription, initiation BP
GO:0071897 DNA biosynthetic process BP
GO:0051103 DNA ligation involved in DNA repair BP
GO:0006310 DNA recombination BP
GO:0000786 nucleosome 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