RetrogeneDB ID: retro_ocun_989

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:37794189..37795288(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP72
• Ensembl ID: ENSOCUG00000012226
• Aliases: None
• Description: signal recognition particle 72kDa [Source:HGNC Symbol;Acc:11303]

Sequence

>retro_ocun_989
GAGGAGAGGAAAATAAACCTTTCAGCAGTTGTTGCAGATCAAAGCCTTTGGGAAAAAGTGGTTCCAGAGAACTTGGGCCT
CCAGGAAGCCACACAAGAACTGTGCTACAACACTGCGTATGCACTGATAGGACAGGGCCACCTGAACCAGGCAGCGAAAA
TCCTATAAAAAGCTGTAGATCTGTGCCACCGTTCACTTTCAGAAGCCTGTGATGGGACTGAGGAAGACCCGCAGGCAGAA
CGGCCATCACTCACTGTCAGATGGCCTATATTCTGCAGCTTCAGGGTCGTACAGAGGGGGCATTGCAACTTTGCAATCGG
ATAATATAATTTAAGCCAACAGATGCGGGAGTATTTGCTGTAATTGCAAATAACGTCATTATCATTAAGAAGGACCAAAA
TGTCTTTGACTCCAAGAAGAAGGTGAAATTACCCAGTGCAGAAAGCGTGGAGTTTAAGCTTTCCAAGAAATAACTGCAAA
CTATAGAATTTAATAAAGCTTCACTTGCTGTGTACACAAACCAGGCAGAACAGTGCCACAAAATAGCTGCCAGTTTACAG
TCCCAAAGCCCTGAGCACCTCCTGCCGGTGTTAATCCAAGCTGCCCAGCTCTGCCATGAAAAGCAGCACACAAAAGCAAC
AGAGCTGCTTCAGGAATTGTCAGATGGGCATCCAGAAAGTGCAACTGCAATTCAGTTGCCCATGGCACAGTTGAAAATTT
CCCAAGGTAATATTTCCAAAGCATGGCTCATATTGAGAAACATACAGAAGTTCAAGCACAAACCAGGCATGGTATCTGCC
TTGGTGACCATGTACAGCCAGGAAAATATTGACAGTGCCATTGAGGTCCTCACCCAAACTATCCAGTGTATCAAAACCAT
CAACCCAAATCTCCTGCTCATCTGTTCTTGCTAAGAGAAGCTAAAACTTCAAACTCAAATATGGGCGGAAGAAGGAGGTA
AGTGGTGACCTAGAACAGCTCTGGAAACAAAATCCCAGACATTCGCACCCTGGCGCAGCTTATTTCTGCTTATTCACTTG
TAGATCCAGAGAAAGCAAACATTCTTACTAAACACTTGCCCTCATCAGACAGTATCTCT

Alignment

ORF - retro_ocun_989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.66 %
• Parental protein coverage: 54.99 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EERKTNLSAVVAAQSNWEKVVPENLGLQEGTHELCYNAACALIGQGHLNQAMKILQKAEDLCRHSFSEDS
          EERK.NLSAVVA.QS.WEKVVPENLGLQE.T.ELCYN.A.ALIGQGHLNQA.KIL.KA.DLC..S.SE..
Retrocopy EERKINLSAVVADQSLWEKVVPENLGLQEATQELCYNTAYALIGQGHLNQAAKIL*KAVDLCHRSLSEAC

Parental  DVTEEDPEAE-LAIIHGQMAYILQLQGRTEEALQLYNQIIKLKPTDVGLLAVIANNIITINKDQNVFDSK
          D.TEEDP.AE..AI.H.QMAYILQLQGRTE.ALQL.N.II..KPTD.G..AVIANN.I.I.KDQNVFDSK
Retrocopy DGTEEDPQAE<TAITHCQMAYILQLQGRTEGALQLCNRII*FKPTDAGVFAVIANNVIIIKKDQNVFDSK

Parental  KKVKLTNAEGVEFKLSKKQLQAIEFNKALLAMYTNQAEQCRKISASLQSQSPEHLLPVLIQAAQLCREKQ
          KKVKL..AE.VEFKLSKK.LQ.IEFNKA.LA.YTNQAEQC.KI.ASLQSQSPEHLLPVLIQAAQLC.EKQ
Retrocopy KKVKLPSAESVEFKLSKK*LQTIEFNKASLAVYTNQAEQCHKIAASLQSQSPEHLLPVLIQAAQLCHEKQ

Parental  HAKAIELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIEKLKHKPGMVSALVTMYSHEEDID
          H.KA.ELLQE.SD.HPE.A..I.L.MAQLKISQGNISKA.LILR.I.K.KHKPGMVSALVTMYS..E.ID
Retrocopy HTKATELLQELSDGHPESATAIQLPMAQLKISQGNISKAWLILRNIQKFKHKPGMVSALVTMYS-QENID

Parental  SAIEVFTQAIQW-YQNQQPKSPAHLSLIREAANFKLKYGRKKEAISDLEQLWKQNPKDIHTLAQLISAYS
          SAIEV.TQ.IQ..YQN.QPKSPAHL.L.REA.......G................P.DI.TLAQLISAYS
Retrocopy SAIEVLTQTIQC<YQNHQPKSPAHLFLLREAKTSNSNMGGRRR*VVT*NSSGNKIP-DIRTLAQLISAYS

Parental  LVDPEKAKALSKHLPSSDSMS
          LVDPEKA..L.KHLPSSDS.S
Retrocopy LVDPEKANILTKHLPSSDSIS

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	0.00 RPM	84.44 RPM
SRP017611_kidney	0.00 RPM	82.10 RPM
SRP017611_liver	0.00 RPM	49.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_989 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_989 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017998	1 retrocopy	retro_cjac_2538,
Homo sapiens	ENSG00000174780	2 retrocopies	retro_hsap_1939, retro_hsap_3685,
Nomascus leucogenys	ENSNLEG00000008806	1 retrocopy	retro_nleu_2909,
Oryctolagus cuniculus	ENSOCUG00000012226	1 retrocopy	retro_ocun_989 ,
Rattus norvegicus	ENSRNOG00000002100	1 retrocopy	retro_rnor_587,