Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable E3 ubiquitin-protein ligase HERC2.

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 g12207 g12207.t1 TSS g12207.t1 21754913 21754913
chr_1 g12207 g12207.t1 isoform g12207.t1 21755403 21758858
chr_1 g12207 g12207.t1 exon g12207.t1.exon1 21755403 21755802
chr_1 g12207 g12207.t1 cds g12207.t1.CDS1 21755403 21755802
chr_1 g12207 g12207.t1 exon g12207.t1.exon2 21755863 21758858
chr_1 g12207 g12207.t1 cds g12207.t1.CDS2 21755863 21758858
chr_1 g12207 g12207.t1 TTS g12207.t1 NA NA

Sequences

>g12207.t1 Gene=g12207 Length=3396
ATGTGGCTACGAAAACTCGAATATTTAGACGAAAAGTGGCTAAAATGCAATTTAAATGCG
GCCTTAAAAGATCAATATTTTACCCGTGCAGCCATTTTCAATACCCTCATACAAGATTCT
GAAATATCTGATACGAAATTTCAACCCGTTGTTAACTCATCAGGACGAAATTCATATTTG
AGGAGTGATGGAAAATATTATTGTGGAGCTAAAATTCTCAATTGTTCTTGCTGTGACGGC
GTTTGTGGTCCTGCGTCATCATGCGTTTGTGATTCGTGTCAATTAGTTCCAGCTTCACTT
GAGCTGCCTGATGATTTTCAAAATCATCAAGAAAAGGCTAATGATTTTTCATTTAGTAGT
GAATCATGCTTTGAATCGTGGATGTGGGGTCCTATTCCAGATGACAACCAACTCAATACA
TGCATAAAAAAACTTCTTGCTGAACAAAGAAAAATTTGTCTCCAAGCAAGCGAAAATAGT
CTTTCAAGTTTCTCATTGAAGATGATTCTTTGCATTTATGAACGCTATTTCGTTGCATTG
TCAAGAAGCAAATGCACAAAAAGCACAGCAAATAATAGAGAAAGCTTATACATTGATGAT
AAAAGCAGAAATTATGAAAATGAAACCAAAGAAATTCCGCTCAGTAAGAGCGAAAAAGTA
AAACACGAGCTTGCAAAAATTGGAACAAGAACTGCATTAAATTTTTTCTTTACAAGTTTA
AAGAGAGCATGGAAGTCTGGCGACACTGAATTATGCAGTGAACTTTTAAGTGATACACTT
GAAGCTATTCAATTGTCGCTTGAACCTGGTGGATTGTTTGATACATCTAGTGTATCAACT
TTATGGATGGAAGCGATAGAAAAGTCTATAAAATTTTTGAGGCAAATTGTATGTAATGAA
AGTGAAGGTGAACAACAAATTCCAAAACCAGATAGAAATATTGCACTCAATTTATTATTA
GAACTTGAAATGCAAAAAGGAAATTTAGCTGGCTCACTTGAAGGGGTTTTATTGCTTTTA
ACTGTAGCTGAAATGAGTCATAATAATAGTGATAATCGTCAAACACCACTAAGTTCTAAT
GGCATTCCTTTAGTAAAGATATTATGCCGCTATAGCGAAATTAATAAAGATAATTCTTAT
CTAACAACCTCTGATCATCATTCCTTCAGTCCAACTGAATCTTTTCTAAGATTTCTTTCA
CTTCCCGATGGCGAAGAGATCGAAGAAGATTTAATTGATCCACAACAAGCAGCTGTCATT
ATTATGAGTCATCTCGATCGTCTTTGTCGCTCTCATTTACCTAGCAAAATATGGACGTCA
AGAATTCAAAATTATCGAAATCAACAAATTATTTCACTCGGTTATAATGGTCTATCACCT
GAATTTAATATTTTTTCCTCAGAATCAGAAGATAAATGGATGTATGATTATACAAGAAAT
TCAAACTATTCTGCACCAACGATTGATTTCGGTGCAAATATTGTCGTTGATCAGATTGCA
TGCTCTGAAAATACTATTTTACTTTTGAGCACAACAGGTGAAGTTTATGAAGTCAAACTT
CATTCTGATCAAACAAAAGCGACAAAAGTTGATGGCTTTGATTCAACTGTGAGCAAAATA
TTTTCTCATTGTGAAGGAAAACATTTTATTGCAATCACAAGCAATAATGAAGTGTATTCA
TGGGGTTGTGGTGATAATGGAAGACTTGGTTTAGGCGATGATAATTTGTCAATGCAGAAA
CCAACTAAAATAACAGCATTAAGTGATAAACAAGTTGTTGGAGCTTCATGTGGAGCAAAT
TATAGTGCTGTCTTTACTAACCATGGTGAATTGTACACATTTGGTCATGGTCTTTATGGA
AAACTTGGTCATGGCAGTTCAGATGATAAGAATGTTCCAACATTAGTAAATGCGCTGAAA
TCTCATAAAATTATTGATGTTGCATGTGGTGATACTCATACACTTTGTGTTAATGATCAA
GGAAAAGTTTTTGCATTTGGTGATTGTGATTTTGGCAAGTTAGGAGTTGGTACAACAAAT
GGCGCTCAAGTTCCAATTTTAGTTGAAAGTTTGAGCAATATCAAGAATGTTTATTGTGGT
TCACACTTTAGCATGGCAATTTCATGTGATGGCAATTCAATTTACACTTGGGGAAAAAAT
GGACGACTTGGACATGAAAATATCATTGAAGATCTTTACGTACCAAAAAAAATTGAAGGT
TTGAATGGAAAGAAAGTTGAGAAAGTTTCAGTTGGATCAACACATTGTTTGCTATTGATG
GAAAATGGTGAACTTTTTGGCTTTGGAAAAAATGATTTTCAACAAATTTGTCCACCTTGC
ATTACTAAAGATACAGTAATTGCAAAACCAATTTTAACAACTCCGCCATTCTTAAAAATA
AGTGGAATTTCATGTGGTTCTACACAGAGTATTATTTGGTCACACTCAGCAATGATTTGC
ATTCCACCACGAATTCCTTTTGTCGTTGATTTGAGCGAACAAACATTTAGACTTCTTGAT
CAACTTTTGTCATGTGTTTGTGGTAATATTCAAGCAAATGCATCAGCTCAAACAACTAAT
AATGGACATCCTCCTAATCAAGAAGCAGAATGCATTGCTGTTGCTTCTTTAAATCTCATG
TGTTTACAATTTCATGCAATGATTTGTAATAATATTTCGCCAAAGAAAGTCGGATTAACT
GGAGCAAGATTAAAAAGCATCAAATCAAGAATTTTACAACTTTCTGGTGGAAATTCAATT
TTAAAAACAATTCAAGAGGCTGCTCAAAGTGCTTTACAAGTTGGTTGGTCAATTTTACTA
CCAACACCATCAGAACGAGCTCAAACTTTGACATCACTTCTTCCTGATCCATCACAAGCC
TCAGCACATCGATTTATGACTGATTTATTAGTTGGTTCTATTATGGCGGAAGGTGGACTA
GAAACAGCATTGAATCAAATTATTCATAGTGAAAGTCATGATTGTGAGCAACTTCCTTTA
CTCGATCTTCTTAAACAACTTCTTCATAACAATTCAACACTCACACAAACTCGATTAAAT
CAATTATTAATTGAAAATCTTACTAAAACAAATGATGAATTGATAATCACTGATACTTCA
TCACCAAGTATTGATTTGCTTCATAAATTTCAACGTCTTTTGTTGTCTCATATTTGTGCT
GCTAGCAACATTGGAAATGATCTTTCTGGTGCTGAATCGTTGCTGGAATCTTACATAATT
TTGATGTCATCATTGTGTGTTTCTACATTAACAAAAGCACAAGAAGTGATCATGCAAGAA
AAGGAAAATGTTGCAATAATTCTACAATGCGATATTTCTGATTCACTACTTTATGAGCTG
TTGTTAGGATTGATACTGGTTCAGAAAGAAAGGTGA

>g12207.t1 Gene=g12207 Length=1131
MWLRKLEYLDEKWLKCNLNAALKDQYFTRAAIFNTLIQDSEISDTKFQPVVNSSGRNSYL
RSDGKYYCGAKILNCSCCDGVCGPASSCVCDSCQLVPASLELPDDFQNHQEKANDFSFSS
ESCFESWMWGPIPDDNQLNTCIKKLLAEQRKICLQASENSLSSFSLKMILCIYERYFVAL
SRSKCTKSTANNRESLYIDDKSRNYENETKEIPLSKSEKVKHELAKIGTRTALNFFFTSL
KRAWKSGDTELCSELLSDTLEAIQLSLEPGGLFDTSSVSTLWMEAIEKSIKFLRQIVCNE
SEGEQQIPKPDRNIALNLLLELEMQKGNLAGSLEGVLLLLTVAEMSHNNSDNRQTPLSSN
GIPLVKILCRYSEINKDNSYLTTSDHHSFSPTESFLRFLSLPDGEEIEEDLIDPQQAAVI
IMSHLDRLCRSHLPSKIWTSRIQNYRNQQIISLGYNGLSPEFNIFSSESEDKWMYDYTRN
SNYSAPTIDFGANIVVDQIACSENTILLLSTTGEVYEVKLHSDQTKATKVDGFDSTVSKI
FSHCEGKHFIAITSNNEVYSWGCGDNGRLGLGDDNLSMQKPTKITALSDKQVVGASCGAN
YSAVFTNHGELYTFGHGLYGKLGHGSSDDKNVPTLVNALKSHKIIDVACGDTHTLCVNDQ
GKVFAFGDCDFGKLGVGTTNGAQVPILVESLSNIKNVYCGSHFSMAISCDGNSIYTWGKN
GRLGHENIIEDLYVPKKIEGLNGKKVEKVSVGSTHCLLLMENGELFGFGKNDFQQICPPC
ITKDTVIAKPILTTPPFLKISGISCGSTQSIIWSHSAMICIPPRIPFVVDLSEQTFRLLD
QLLSCVCGNIQANASAQTTNNGHPPNQEAECIAVASLNLMCLQFHAMICNNISPKKVGLT
GARLKSIKSRILQLSGGNSILKTIQEAAQSALQVGWSILLPTPSERAQTLTSLLPDPSQA
SAHRFMTDLLVGSIMAEGGLETALNQIIHSESHDCEQLPLLDLLKQLLHNNSTLTQTRLN
QLLIENLTKTNDELIITDTSSPSIDLLHKFQRLLLSHICAASNIGNDLSGAESLLESYII
LMSSLCVSTLTKAQEVIMQEKENVAIILQCDISDSLLYELLLGLILVQKER

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12207.t1 Gene3D G3DSA:2.130.10.30 - 472 827 0.0000000
5 g12207.t1 PANTHER PTHR22870:SF398 E3 UBIQUITIN-PROTEIN LIGASE HERC2 537 772 0.0000000
7 g12207.t1 PANTHER PTHR22870 REGULATOR OF CHROMOSOME CONDENSATION 537 772 0.0000000
6 g12207.t1 PANTHER PTHR22870:SF398 E3 UBIQUITIN-PROTEIN LIGASE HERC2 696 826 0.0000000
8 g12207.t1 PANTHER PTHR22870 REGULATOR OF CHROMOSOME CONDENSATION 696 826 0.0000000
12 g12207.t1 PRINTS PR00633 Chromosome condensation regulator RCC1 signature 610 626 0.0000000
10 g12207.t1 PRINTS PR00633 Chromosome condensation regulator RCC1 signature 644 657 0.0000000
9 g12207.t1 PRINTS PR00633 Chromosome condensation regulator RCC1 signature 663 679 0.0000000
11 g12207.t1 PRINTS PR00633 Chromosome condensation regulator RCC1 signature 749 765 0.0000000
1 g12207.t1 Pfam PF00415 Regulator of chromosome condensation (RCC1) repeat 557 604 0.0000000
2 g12207.t1 Pfam PF00415 Regulator of chromosome condensation (RCC1) repeat 609 657 0.0000000
3 g12207.t1 Pfam PF00415 Regulator of chromosome condensation (RCC1) repeat 661 707 0.0000001
4 g12207.t1 Pfam PF00415 Regulator of chromosome condensation (RCC1) repeat 713 759 0.0000000
15 g12207.t1 ProSiteProfiles PS50012 Regulator of chromosome condensation (RCC1) repeat profile. 556 608 15.4490000
18 g12207.t1 ProSiteProfiles PS50012 Regulator of chromosome condensation (RCC1) repeat profile. 609 660 16.2530000
17 g12207.t1 ProSiteProfiles PS50012 Regulator of chromosome condensation (RCC1) repeat profile. 661 710 12.8960000
16 g12207.t1 ProSiteProfiles PS50012 Regulator of chromosome condensation (RCC1) repeat profile. 712 762 11.2480000
13 g12207.t1 SUPERFAMILY SSF50985 RCC1/BLIP-II 488 816 0.0000000

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 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.

Raw TPM values