RetrogeneDB ID: retro_ocun_592

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:1102263..1103119(+)
• Located in intron of: ENSOCUG00000009345

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ERP44
• Ensembl ID: ENSOCUG00000004220
• Aliases: None
• Description: endoplasmic reticulum protein 44 [Source:HGNC Symbol;Acc:18311]

Sequence

>retro_ocun_592
AGAGAATACAGAGGTCAGTGATCAGTGAAAGTACTTGCAGATTACATCAGGCAACAAAAAAATGACCCAATTCAAGAAAC
TCAGGATTTAGCAGAAATCAACCCTCTTGATCACAGAAAAAGAAATACCATCGAGTATTTTGAACAAAAGGATTCAGACA
ACTATAGAGTATTTGAAAGAGTAGTAAGTATTTTGCATGATGACTGTGCCTTCCTTTCTGTATTTGGGGATGTTTCAAAA
CCAGAAAGATACAGTGGAGGCAGCATCATCTACAACCACCCGAGCATTCTGCCCCAGATACGGTGTACTCAGGATCCATG
GCAGGTTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACCTTTGAAAATGGAGA
GGAGTTGACAGAATGTTTGCCATTTCTTCTATTCTTCCATATGAGAGACAATGCAGAAAGCTTAGAAATACTCCAGAATG
AAGTAGCCCGGCAACTAATAAGTGAAAAAGATACAGTCAACTTTTTGCATGCAGATTGTGACCAATTTAGACGTCCTCTT
GTGCACGTACAGAAACTCCAGCAGGTTGCCCTGTCAGAGCAGTTGATAGCTTCAGGCATATGTATGTGTTTGCAGACTTC
AAGGATGTTTTAATTCCTGGTAACTCAAGGAGCTTGTATTTGACTTACACTCTGGAAAACTCCACAGAGCATCCCATCAT
GGGCCTGACCCAACTGATACAGCTTCCAGAGAGCAAGTCCAAGATGTGGCAGGCAGTACGTCCACCCGAGAGCTCCTTCC
AGAAACTAGCACCCAGCAAATATAGGCATGCTTTAGTGAGAGGTCAAGACGAGCTT

Alignment

ORF - retro_ocun_592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.38 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  REYRGQRSVKALADYIRQQKSDPIQEIQDLAEINSLDRSKRNIIGYFEQKDSDNYRVFERVASILHDDCA
          REYRGQ.SVK.LADYIRQQK.DPIQE.QDLAEIN.LD..KRN.I.YFEQKDSDNYRVFERV.SILHDDCA
Retrocopy REYRGQ*SVKVLADYIRQQKNDPIQETQDLAEINPLDHRKRNTIEYFEQKDSDNYRVFERVVSILHDDCA

Parental  FLSAFGDVSKPERYSGDNIIY-KPPGHSAPDMVYLGSMTNFDVTYNWIQDKCVPLVREITFENGEELTEE
          FLS.FGDVSKPERYSG..IIY..PP.HSAPD.VY.GSM..FDVTYNWIQDKCVPLVREITFENGEELT.E
Retrocopy FLSVFGDVSKPERYSGGSIIY<QPPEHSAPDTVYSGSMAGFDVTYNWIQDKCVPLVREITFENGEELT-E

Parental  GLPFLILFHMKDDTESLEIFQNEVARQLISEKGTVNFLHADCDKFRHPLLHIQK-TPADCPVIAIDSFRH
          .LPFL..FHM.D..ESLEI.QNEVARQLISEK.TVNFLHADCD.FR.PL.H.QK.TPA.CPV.A.DSFRH
Retrocopy CLPFLLFFHMRDNAESLEILQNEVARQLISEKDTVNFLHADCDQFRRPLVHVQK<TPAGCPVRAVDSFRH

Parental  MYVFENFKDVLIPGK-LKQFVFDLHSGKLHREFHHGPDPTDRAPGEQVQDVASSP-PESS-FQKLAPSEY
          MYVF..FKDVLIPG..LK..VFDLHSGKLHR..HHGPDPTD.A..EQVQDVA.S..P..S.FQKLAPS.Y
Retrocopy MYVFADFKDVLIPGN<LKELVFDLHSGKLHRASHHGPDPTDTASREQVQDVAGST>PPESSFQKLAPSKY

Parental  RYTLLRDRDEL
          R..L.R..DEL
Retrocopy RHALVRGQDEL

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	0.06 RPM	60.21 RPM
SRP017611_kidney	0.10 RPM	59.19 RPM
SRP017611_liver	0.00 RPM	47.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_592 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_592 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000004220	1 retrocopy	retro_ocun_592 ,
Ochotona princeps	ENSOPRG00000000004	1 retrocopy	retro_opri_852,
Sarcophilus harrisii	ENSSHAG00000012181	1 retrocopy	retro_shar_360,