RetrogeneDB ID: retro_ocun_1126

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:162915329..162916558(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000004846
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJA2
• Ensembl ID: ENSOCUG00000004839
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 2 [Source:HGNC Symbol;Acc:14884]

Sequence

>retro_ocun_1126
ATAGCGAACGTGGCCGACACGAAGTGTAGGACATCCCGGGCGTCCCGCCTGGCACCAGCGAGAATGAGCTGAAGAAGGCA
TCCAGAAAGTTAGCCAAGGAATACCCTCCTGATAAGAATCCAAATGCTGGAGACAAATTCAAAGAAATAAGCTTTGCATA
TGAAGTTCTATCAAATCCCGAGAAGCGTGAATTGTATGACAGATATGGAGAACAAGGGCTTCGGGAAGGTAGTGGCGGCG
GTGGTGTCATGGATATTTTCTCTCACATTTTTGGTGGGGGATTGTTTGGCTTTATGGGCAATCAGAGTAGAAGTCGAAAT
GGCAGAAGAAGAGGAGAGGACATGATGCATCCACTCAAAGTATCTTTAGAAGATCTGTATAATGGCAAGACAACCAAACT
ACAACTTAGCAAGAATGTACTCTGCAGTGCGTGCAGCGGCCAAGGTGGAAGTCTGGAGCAGTTCAGAAGTGCAGTGCTTG
TCGAGGTCAAGGTGTACCCATCATGATCAGACAGCTGGCTGCAGGGATGGTACAGCAGATGCAGTCTGTGTGCTCTGATT
GCAAAGGCGAAGGAGAAGTAGTTAATGAAAAGGACCGCTGTAAAAAATGCGAAGGGAAGAAGATGATTAAAGAAGTCAAA
ATTCTTGCAGTCCATGTAGACAAAGGCATGAAACACGGACAGAGAATTACACTCACTGGGGAAGCAGACCAGGCTCCTGG
GGTGGAACCAGGGGACATTGTTCTTTTGCTGCAGGAAAAAGAACATGAGGTGTTCCAGAGAGATGGGAATGATTTACATG
TGACATATAAGATAGGACTTGTTGAAGCCCTGTGTGGATTTCAGTTCACATTTAAGCACCTTGATGCCCGGCAGATTGTG
GTGAAATACCCTCCTGGCAAAGTCATTGAACCAGGATGTGTTCGTGTAGTTCGAGGTGAAGGAATGCCACAGTATCCTAA
TCCCTTTGAAAAGGGGGATCTTTACATAAATTTTGATGTGCAGTTTCCTGAAAACAACTGGATCAACCCAGACAAGCTTT
CTGAACTAGAAGATTTCTGCCATCTAGACCAGAAGTTCCTAACATAATTGGAGAAACGGAGGAGGTAGAGCTTCAGGAAT
CTGATAGCACACGAGGCTCAGGAGGTGGTCAGAGGCGCGAGGCCTACAATGATAGCTCTGATGAGGAAGCAGCAGCCATC
ATGGACCTGGAGTGCAGTGTGCCCATCAG

Alignment

ORF - retro_ocun_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MANVADTKLY-DILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRY
          .ANVADTK...DI.GVPPG.SENELKKA.RKLAKEY.PDKNPNAGDKFKEISFAYEVLSNPEKRELYDRY
Retrocopy IANVADTKCR<DIPGVPPGTSENELKKASRKLAKEYPPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRY

Parental  GEQGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSK
          GEQGLREGSGGGG.MD.IFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSK
Retrocopy GEQGLREGSGGGGVMD-IFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSK

Parental  NVLCSACSGQGG-KSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEGK
          NVLCSACSGQGG.KSGAVQKCSACRG.GV.IMIRQLA.GMVQQMQSVCSDC.GEGEV.NEKDRCKKCEGK
Retrocopy NVLCSACSGQGG<KSGAVQKCSACRGQGVPIMIRQLAAGMVQQMQSVCSDCKGEGEVVNEKDRCKKCEGK

Parental  KVIKEVKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVEA
          K.IKEVKIL.VHVDKGMKHGQRIT.TGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLH.TYKIGLVEA
Retrocopy KMIKEVKILAVHVDKGMKHGQRITLTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHVTYKIGLVEA

Parental  LCGFQFTFKHLDARQIVVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDKL
          LCGFQFTFKHLDARQIVVKYPPGKVIEPGCVRVVRGEGMPQY.NPFEKGDLYI.FDVQFPENNWINPDKL
Retrocopy LCGFQFTFKHLDARQIVVKYPPGKVIEPGCVRVVRGEGMPQYPNPFEKGDLYINFDVQFPENNWINPDKL

Parental  SELED-LLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSDEE-SSSHHGPGVQCAHQ
          SELED..LPSRPEVPNIIGETEEVELQE.DSTRGSGGGQRREAYNDSSDEE.SSSHHGPGVQCAHQ
Retrocopy SELED<FLPSRPEVPNIIGETEEVELQESDSTRGSGGGQRREAYNDSSDEE<SSSHHGPGVQCAHQ

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	0.17 RPM	137.36 RPM
SRP017611_kidney	0.10 RPM	87.07 RPM
SRP017611_liver	0.15 RPM	48.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1126 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1126 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003757	3 retrocopies	retro_btau_1215, retro_btau_1625, retro_btau_798,
Cavia porcellus	ENSCPOG00000006955	1 retrocopy	retro_cpor_1466,
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126 ,
Rattus norvegicus	ENSRNOG00000016251	1 retrocopy	retro_rnor_2778,