RetrogeneDB ID: retro_ocun_1516

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:74815296..74816584(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSOCUG00000003871
• Aliases: None
• Description: Aspartate aminotransferase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P12345]

Sequence

>retro_ocun_1516
ATGGCCCTGCTGCACTCTGCCCACGTCCTCTCCGGGGTAGCCTCCACCTTCTACCCAGGCCTCGCCACCGCAGCCTCTGC
CAGAGCCAGCTCCTGGTGGGCCCATGTGGAGATGGGACCCCCAGATCCTATCGTGGGAGTTACAGAAGCCTACAAGAGAT
ACACAAACAGCAAAAAGATGAATCTGGGAGTTGGCGCCTACCGGGATGATAACGGGAGGCCTTACATACTCCCTAAGTCG
GGAAGGCAGAGGCTCAGATCGCTGCAAAAGGTCTCGACAAGGAACACCTGCCCATGGGGGGACTGCTGAGTCCTGTAGGG
CATCAGCAGAACTAGCCCTGGGCGAGAACAGCGAAGTGGTGAAAAGCGGCCGTTTTGTCACCGTGCAAACCATCTCTGGA
ACGGGGGCCCTAAGGATAGGAGCCAGTTTTCTGCAAAGGTTTTTCAAGTTCAGCCAAGATGTCTTTCTGCCCAAACCATC
CTGGGGAAATCACACACCCATCTTCAGGGATGCTGGCATGCAGCTACAAAGCTATCGGTACTATGACCCCAAGACTTGCG
GTTTTGACTTCACAGGCGCCCCTGGAGGACATCTCAAAAATTCCAGAGCAAAGTGTTCTCCTGTTGCATGCCTGTACCCA
CAATCCCACAAGAGTGGATCCTCGGCCTGAGCAGTGGAAGGAAATAGCAACAGTGGCGAAGAAAAGGAATCTGTTCGCGT
TCTTTGACCTGGCCTACCAAGGCTTTGCCAGTGGTGACGGTGACAAGGACGCCTGGGCTGTGCGCCACTTCATTGAACAG
GGCATTAATGTGTGTCTCTGCCAGTCATATGCCAAGAACATGGGCTTATATGGTGAACGTGTTGGAGCCTTCACTGTGAT
CTGCGAAGATGCAGATGAAGCCAAAAGGGTGGAGTCGCAGTTGAAGATCTTGATCCGTCCGATGTATTCCAACCCTCCTA
TCAATGGGGCCCGGATTGCCTCCACAATTCTGACTTCCCCCGATGTGCGAAAGCAATGGTTGCAGGAAGTGAAAGGCATG
GCAGACCACATCATTGGCATGCGGACCCAGCTGGTCTCCAACCTCAAGAAGGAAGGCTCCACCCACAACTGGCAGCACAT
CACCAACCAGATTGGCATGTTTTGTTTCACAGGACTAAAGCCTGAACAGGTGGAGCGGCTGACCAAGGAGTTCTCCATCT
ACATGACAAAGACGATCACATCTCTGTGGCTGGCATCACTTCTGTCAATGTGGGCTACCTTGCCCATGCCATTCACCAGG
TCACCAAG

Alignment

ORF - retro_ocun_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDD
          MALLHSA.VLSGVAS.F.PGLA.AASARASSWWAHVEMGPPDPI.GVTEAYKR.TNSKKMNLGVGAYRDD
Retrocopy MALLHSAHVLSGVASTFYPGLATAASARASSWWAHVEMGPPDPIVGVTEAYKRYTNSKKMNLGVGAYRDD

Parental  NGKPYVLPS-VRKAEAQIAAKGLDKEYLPIGGL-AEFCRASAELALGENSEVVKSGRFVTVQTISGTGAL
          NG.PY.LP..V.KAEAQIAAKGLDKE.LP.GGL.AE.CRASAELALGENSEVVKSGRFVTVQTISGTGAL
Retrocopy NGRPYILPK<VGKAEAQIAAKGLDKEHLPMGGL<AESCRASAELALGENSEVVKSGRFVTVQTISGTGAL

Parental  RIGASFLQRFFKFSRDVFLPKPSWGNHTPIFRDAGMQLQSYRYYDPKTCGFDFTGA-LEDISKIPEQSVL
          RIGASFLQRFFKFS.DVFLPKPSWGNHTPIFRDAGMQLQSYRYYDPKTCGFDFTGA.LEDISKIPEQSVL
Retrocopy RIGASFLQRFFKFSQDVFLPKPSWGNHTPIFRDAGMQLQSYRYYDPKTCGFDFTGA>LEDISKIPEQSVL

Parental  LLHACAHNPTGVDPRPEQWKEIATVVKKRNLFAFFDMAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSY
          LLHAC.HNPT.VDPRPEQWKEIATV.KKRNLFAFFD.AYQGFASGDGDKDAWAVRHFIEQGINVCLCQSY
Retrocopy LLHACTHNPTRVDPRPEQWKEIATVAKKRNLFAFFDLAYQGFASGDGDKDAWAVRHFIEQGINVCLCQSY

Parental  AKNMGLYGERVGAFTVICKDADEAKRVESQLKILIRPMYSNPPIHGARIASTILTSPDLRKQWLQEVKGM
          AKNMGLYGERVGAFTVIC.DADEAKRVESQLKILIRPMYSNPPI.GARIASTILTSPD.RKQWLQEVKGM
Retrocopy AKNMGLYGERVGAFTVICEDADEAKRVESQLKILIRPMYSNPPINGARIASTILTSPDVRKQWLQEVKGM

Parental  ADRIIGMRTQLVSNLKKEGSTHSWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMT-KDGRISVAGVTSG
          AD.IIGMRTQLVSNLKKEGSTH.WQHIT.QIGMFCFTGLKPEQVERLTKEFSIYMT.KD..ISVAG.TS.
Retrocopy ADHIIGMRTQLVSNLKKEGSTHNWQHITNQIGMFCFTGLKPEQVERLTKEFSIYMT<KDDHISVAGITSV

Parental  NVGYLAHAIHQVTK
          NVGYLAHAIHQVTK
Retrocopy NVGYLAHAIHQVTK

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	1.16 RPM	103.64 RPM
SRP017611_kidney	1.11 RPM	101.96 RPM
SRP017611_liver	1.77 RPM	164.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1516 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516 ,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,