RetrogeneDB ID: retro_ocun_1419

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:64571001..64572110(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026412
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2Q2
• Ensembl ID: ENSOCUG00000022720
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2Q family member 2 (UBE2Q2), mRNA [Source:RefSeq mRNA;Acc:NM_001082694]

Sequence

>retro_ocun_1419
ATGTCCGTGTCAGGGCTGAAGGCCGAGCTGAAGTTCCTGGCGTCCATCTTCGACAAGAACCACGAGCGGTTCCGCATCGT
CAGCTGGAAGCTGGATGAGCTGCACTGCCAGTTCCTGGTGCCGCCGCCGGCGCCGCCGCTGCTCATGCTGCACTGCAACA
TCACGGAATCTTACCCCTCTTCTTCACCAATATGGTTTGTCGACTCTGATGACCCAAATCTGACCTCAGTTCTGGAGCGT
CTTGAAGATTCTAAGAACAACAATTCGCTTCGTCAGCAATTGAAGTGGTTGATATGTGAACTCTGCAGATTATATAACCT
TCCTAAGCACCTGGATGTTGAGATGCTAGATCAACCACTGCCCACGGGTCAGAATGGGACAAAAGAGGAAGTCGCTTCAG
AAGAGGAGGAAGAGGAAGAGATGGCGGAAGATATAGAAGACTTAGATCACTATGAGATGAAGGAAGAAGAGCCTATTAAT
GGGCTCAGTCAGAGGATGAAGGAATTGAAAAAGAAAACTTGGCCATATTAGAGAAGATTAGGAAGAGTCAAAGGCAAGAC
CATTTAAATGGTGCGGTGTCTGGGTCAGTGCAAGCTTCAGACAGACTGATGAAAGAGCTCAGGGACATATACAGATCACA
GAGTTACAAGACAGGGATTTATTCAGTGGAACTGATAAATGACAGTTTATATGACTGGCACGTTAAACTACAGAAGGTTG
ACCCTGATAGTCCTTTGCACAGTGATCTTCAAATCTTAAAAGAAAAAGAAGGCGGCATAGAATATATTTTGCTTAACTTC
TCTTTTAAGGATAACTTTCCGTTTGATCCTCCATTTGTCCGAGTGGTGTTACCTGTTCTCTCAGGAGGGTATGTGTTGGG
CGGAGGAGCATTGTGTATGGAACTTCTCACAAAACAGGGCTGGAGCAGTGCCTACTCGATAGAATCGGTCATCATGCAAA
TAGATGCCACCCTAGTCAAAGGCAAAGCCAGAGTGCAGTTTGGAGCAAATAAGAATCAGTATAATCTAGCAAGAGCCCAA
CAGTCCTATAATTCCATTGTACAGATACATGAGAAAAATGGCTGGTACACCCCTCCAAAGGAAGATGGC

Alignment

ORF - retro_ocun_1419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVSGLKAELKFLASIFDKNHERFRIVSWKLDELHCQFLVPPPAPPLLTLHCNITESYPSSSPIWFVDSD
          MSVSGLKAELKFLASIFDKNHERFRIVSWKLDELHCQFLVPPPAPPLL.LHCNITESYPSSSPIWFVDSD
Retrocopy MSVSGLKAELKFLASIFDKNHERFRIVSWKLDELHCQFLVPPPAPPLLMLHCNITESYPSSSPIWFVDSD

Parental  DPNLTSVLERLEDSKNNNSLRQQLKWLICELCRLYNLPKHLDVEMLDQPLPTGQNGTTEEVTSEEEEEEE
          DPNLTSVLERLEDSKNNNSLRQQLKWLICELCRLYNLPKHLDVEMLDQPLPTGQNGT.EEV.SEEEEEEE
Retrocopy DPNLTSVLERLEDSKNNNSLRQQLKWLICELCRLYNLPKHLDVEMLDQPLPTGQNGTKEEVASEEEEEEE

Parental  MAEDIEDLDHYEMKEEEPING-RKSEDEGIEKENLAILEKIRKSQRQDHLNGAVSGSVQASDRLMKELRD
          MAEDIEDLDHYEMKEEEPING...SEDEGIEKENLAILEKIRKSQRQDHLNGAVSGSVQASDRLMKELRD
Retrocopy MAEDIEDLDHYEMKEEEPING<AQSEDEGIEKENLAILEKIRKSQRQDHLNGAVSGSVQASDRLMKELRD

Parental  IYRSQSYKTGIYSVELINDSLYDWHVKLQKVDPDSPLHSDLQILKEKE-GIEYILLNFSFKDNFPFDPPF
          IYRSQSYKTGIYSVELINDSLYDWHVKLQKVDPDSPLHSDLQILKEKE.GIEYILLNFSFKDNFPFDPPF
Retrocopy IYRSQSYKTGIYSVELINDSLYDWHVKLQKVDPDSPLHSDLQILKEKEGGIEYILLNFSFKDNFPFDPPF

Parental  VRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQINATLVKGKARVQFGANKNQYNLARAQQS
          VRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQI.ATLVKGKARVQFGANKNQYNLARAQQS
Retrocopy VRVVLPVLSGGYVLGGGALCMELLTKQGWSSAYSIESVIMQIDATLVKGKARVQFGANKNQYNLARAQQS

Parental  YNSIVQIHEKNGWYTPPKEDG
          YNSIVQIHEKNGWYTPPKEDG
Retrocopy YNSIVQIHEKNGWYTPPKEDG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.28 RPM	87.42 RPM
SRP017611_kidney	0.20 RPM	61.73 RPM
SRP017611_liver	0.08 RPM	34.84 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1419 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1419 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000032307	3 retrocopies	retro_mmus_156, retro_mmus_3421, retro_mmus_622,
Oryctolagus cuniculus	ENSOCUG00000022720	1 retrocopy	retro_ocun_1419 ,