RetrogeneDB ID: retro_ocun_963

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:4819249..4820203(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LBR
• Ensembl ID: ENSOCUG00000000285
• Aliases: None
• Description: lamin B receptor [Source:HGNC Symbol;Acc:6518]

Sequence

>retro_ocun_963
CCAAGTAGAAAGTTTGCAGATGGTGAAGTGGTAAGAGGTCGGTGGCCCAGAGTTCACTTTATTATGAAGTGGAGATTTTG
AGCCACGATGACAAATCTCAACTATACACTGTAAAATACGAGCATGGAACTGAGCTGGAATTGGAGGAAAGTGACATCAA
ACCTTTAACTACTTTTAAGCAAAATAAAAGTGGCTCAACCTCCAGTTCTCCCTCCAGATGGTGGGGGAGCAAAGGGAGTC
GAGGGAGTCAGTCAAGATCACACTCCCAGGCCCCTGGTTGACCACCTAGAAGTTCCCAAAGATCTGCCTCCACTTCCCAC
CAGCCTGCCATTCAGGAAACAAAGAGGGAAATATTGGAAGTCAAATTGACTCCTCTGGTGTTGAGGCCATTTGGAAATAG
CATCAGCAGATACAATGGGGAAGCAGAGCATGTGGAGTGGAATGTGGAGAAGAATGAGCTGCCTGATAAGAACACACAGG
AAAATTCCATTTACCACAAGGAGCAGTTACGTATCTACACAGTATAGCCTTCATCCTAGAAGAGATCAAATTAAAAAAAC
AGATTTTAATGAAGAAAAACTTGTTACCAAAAGACCTGCATTGTTCAGGACCTATGAAGTGAGCACCACCCAGACAGAGG
ACCTGGAGTTCAGAGGAGTCCCTGGTGTGTTCCTCATCATGATTGGCCTGCCTGTCTTCCTCTTCCTGTTGCTGTTGATG
TGTAAACAGGATGAGTTCAGTCTTCTCAACTTCCCTCCTCCTCTGCCAGCTTGGGATGATTTCTGGGAAATGAGAGTGTT
TGGGGTCTACCTCCTCTGGTTTTTCATTCAAGCTCTGTTCTACCTACTGCCAATTGGGCAGGTTGTAGAAGGAATGCCTC
TTATTAATGGGAGAAGACTCAAGAACAGATTAAATGGTTTCTACGCATTCCTCCTGACATCAGCTGTTGGAGCC

Alignment

ORF - retro_ocun_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.15 %
• Parental protein coverage: 51.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSRKFADGEVVRGRWPG-SSLYYEVEILSHDSKSQLYTVKYKDGTELELKESDIKPLTSFKQRKSGSTSS
          PSRKFADGEVVRGRWP..SSLYYEVEILSHD.KSQLYTVKY..GTELEL.ESDIKPLT.FKQ.KSGSTSS
Retrocopy PSRKFADGEVVRGRWPR<SSLYYEVEILSHDDKSQLYTVKYEHGTELELEESDIKPLTTFKQNKSGSTSS

Parental  SPSRRRGSKGSRGSRSRSRSRSPGRPPRSSRRSASASHQPDIQETRREILEVKLTPLVLKPFGNSISRYN
          SPSR..GSKGSRGS.SRS.S..PG.PPRSS.RSAS.SHQP.IQET.REILEVKLTPLVL.PFGNSISRYN
Retrocopy SPSRWWGSKGSRGSQSRSHSQAPG*PPRSSQRSASTSHQPAIQETKREILEVKLTPLVLRPFGNSISRYN

Parental  GEAEHVERNTERNELPQKNTQE-KFHLPQ-ESSYVSTQYSLRPRREEIKLKETDFNEEKLVTKRPALLRT
          GEAEHVE.N.E.NELP.KNTQE.KFHLPQ..SSYVSTQYSL.PRR..IK...TDFNEEKLVTKRPAL.RT
Retrocopy GEAEHVEWNVEKNELPDKNTQE<KFHLPQ<RSSYVSTQYSLHPRRDQIK--KTDFNEEKLVTKRPALFRT

Parental  YEVSTTQTEDLEFGGVPGVLLLMIGLPVFLFLLLLMCKQDEPSLLNFPPPLPAWGDLWETRVFGVYLLWF
          YEVSTTQTEDLEF.GVPGV.L.MIGLPVFLFLLLLMCKQDE.SLLNFPPPLPAW.D.WE.RVFGVYLLWF
Retrocopy YEVSTTQTEDLEFRGVPGVFLIMIGLPVFLFLLLLMCKQDEFSLLNFPPPLPAWDDFWEMRVFGVYLLWF

Parental  FVQALFYLLPIGKVVEGMPLINGRRLKYRLNGFYAFLLTSAAVGA
          F.QALFYLLPIG.VVEGMPLINGRRLK.RLNGFYAFLLTS.AVGA
Retrocopy FIQALFYLLPIGQVVEGMPLINGRRLKNRLNGFYAFLLTS-AVGA

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	16.61 RPM
SRP017611_kidney	0.00 RPM	14.90 RPM
SRP017611_liver	0.00 RPM	24.51 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_963 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005848	1 retrocopy	retro_mdom_1746,
Oryctolagus cuniculus	ENSOCUG00000000285	1 retrocopy	retro_ocun_963 ,