RetrogeneDB ID: retro_ocun_1257

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:56734535..56735252(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025947
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCBP3
• Ensembl ID: ENSOCUG00000002696
• Aliases: None
• Description: poly(rC) binding protein 3 [Source:HGNC Symbol;Acc:8651]

Sequence

>retro_ocun_1257
GAAATGGACACCGGTGTGATTGAAGGTGGATTAAATGTCACTCTCACCATCCGGCTACTTATGCATGGCAAGGAAGTTGG
TAGTATCATCGGAAAGAAAGGAGAATCTGTTAAGAAGATGCGCGAGGAGAGTGGTGCACGTATCAACATCTCAGAAGGGA
ATTGTCCTGAGAGAATTATCACTTTGGCTGGACCCACTAATGCCATTTTCAAAGCATTTGCTATGATCATTGACAAACTG
GAAGAGGACATCAGCAGCTCTATGACCAATAGCACAGCTGCCAGTAGACCTCCGGTTACCTTGAGGCTGGTGGTTCCTGC
TAGTCAGTGTGGCTCTCTCATTGGAAAAGGTGGTTGCAAGATCAAGGAAATAAGAGAGAGTACAGGGGCTCAGGTGCAGG
TGGCAGGGGATATGCTCCCCAACTCAACTGAGCGGGCCATCACTATTGCTGGCATCCCGCAATCCATCATTGAGTGTGTC
AAACAGATCTGCGTGGTCATGTTGGAGTCCCCTCCGAAGGGCGTGACCATCCCGTACCGGCCCAAGCCGTCCAGTTCTCC
GGTCATCTTTGCAGGTGGTCAGGCCTATACCATTCAAGGACAGTATGCCATTCCACAGCCAGATTTGACCAAGCTGCACC
AGTTGGCAATGCAACAGTCTCATTTTCCTATGACCCATGGCAACACCGGATTCAGTGGCATTGAATCCAGCTCTCCA

Alignment

ORF - retro_ocun_1257 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.08 %
• Parental protein coverage: 68.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMESKVSEGGLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIF
          .M...V.EGGLNVTLTIRLLMHGKEVGSIIGKKGE.VKKMREESGARINISEGNCPERI.T..GPT.AIF
Retrocopy EMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIF

Parental  KAFAMIAYKFEEDIISSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLP
          KAFAMI..K.EEDI.SSM.NS.A.S.PPVTLRLVVPASQCGSLIGKGG.KIKEIRESTGAQVQVAGDMLP
Retrocopy KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP

Parental  NSTERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKPASTPVIFAGGQAYTIQGQYAIPHPDLT
          NSTERA.TI.G.P..II.CVKQICVVMLESPPKG.TIPYRPKP.S.PVIFAGGQAYTIQGQYAIP.PDLT
Retrocopy NSTERAITIAGIPQSIIECVKQICVVMLESPPKGVTIPYRPKPSSSPVIFAGGQAYTIQGQYAIPQPDLT

Parental  KLHQLAMQQTPFPPLGQTNPAFPGLDASPP
          KLHQLAMQQ..F.P....N..F.G...S.P
Retrocopy KLHQLAMQQSHF-PMTHGNTGFSGIESSSP

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	12.97 RPM	20.70 RPM
SRP017611_kidney	18.95 RPM	0.10 RPM
SRP017611_liver	9.94 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1257 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742, retro_dord_748,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257 ,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,