RetrogeneDB ID: retro_ocun_1265

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:19310796..19311807(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022105
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSOCUG00000003458
• Aliases: None
• Description: primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Sequence

>retro_ocun_1265
TATTCCCACAGACCCAGTCAGCACAATACCGTGAAGCTGGGCGCTTTCCAGGCTCAGGAGAAAGAGCTGGTGTTCGACAT
CGACATGACAGACTACGATGACGTGAGGAGATGTTGTAGTTCCGCAGACATTTGTTCCAAGTGCTGGACCCTCATGACCA
TGGCCATACTCATCATCGACCGAGCGTTGAAGGAGGTCTTTGGATTTAAGCATCGTCTCTGGGTGTATTCTGGAAGGAGA
GGTGTTCATTGTTGGGTCTGCGATGAATCGGTTAGGAAATTGTCCTCCACAGTGCGTTCTGGAATAGTTGAGTATTTGAG
TCTTGTAAAGGGCGGTCAAGACGTTAAGAAGAAAGTTCACCTAAATGAAAAAGTTCACCCTTTTGTCAGAAGATCCATAA
ACATAATTAAAAAATACTTTGAAGAATATGCCTTGGTTGGTCAAGATATTCTTGAAAATAAAGAAAGCTGGGATAAGATA
TTAGCCCTTGTTCCTGAAGCAATTCATGCTGATCTTCAACAAGGCTTCCAGAAGTGTCACAGCTCTCTTCAGCGTTGGGA
GCACCTGAAGAAAACAATAGCCAAACATCAGAATAACACCAAAAACGACAAATGTGCACCCTGGCTGGAGTGGGAGATTA
TGCTGCAGTACTGTTTTCCACGGCTGGATATCAATGTTAGCAAAGGAATCAATCATTTACTGAAGAGCCCTTTCAGTGTG
CATCCTAAAACAGGTCGCATTTCTGTGCCCATTAATTTACAGAAAGTGGACCAGTTTGATCCGTTTACTGTTCCAACCAT
AAGCTCCATCTGCCGTGAGTTAGATGCCATTTCCAACAATGAAGAGGAAAAAGAGGAGAATGAAGCTGAATCAGATATCA
AACGTAGAACCAGAGATTATAAGAAGACCAGTCTGGCACCTTATGTCAAAGTTTTTGAACAGTTTCTTGAAAACCTCGAT
AAATCCCGAAAAGGAGAACTCCTCAAGAAGAGTGATTTACAAAAAGATTTC

Alignment

ORF - retro_ocun_1265 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.11 %
• Parental protein coverage: 80.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSHRPSQHSTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAILIIDRALKEDFGFK
          YSHRPSQH.TVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAILIIDRALKE.FGFK
Retrocopy YSHRPSQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAILIIDRALKEVFGFK

Parental  HRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLNEKVHPFVRRSINIIKKYF
          HRLWVYSGRRGVHCWVCDESVRKLSS.VRSGIVEYLSLVKGGQDVKKKVHLNEKVHPFVRRSINIIKKYF
Retrocopy HRLWVYSGRRGVHCWVCDESVRKLSSTVRSGIVEYLSLVKGGQDVKKKVHLNEKVHPFVRRSINIIKKYF

Parental  EEYALVGQDILENKESWDKILALVPEAIHADLQQGFQKCHSSLQRWEHLKKTIAKHQNNTKNDKCAPWLE
          EEYALVGQDILENKESWDKILALVPEAIHADLQQGFQKCHSSLQRWEHLKKTIAKHQNNTKNDKCAPWLE
Retrocopy EEYALVGQDILENKESWDKILALVPEAIHADLQQGFQKCHSSLQRWEHLKKTIAKHQNNTKNDKCAPWLE

Parental  WEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPINLQKVDQFDPFTVPTISSICRELDAISNN
          WEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPINLQKVDQFDPFTVPTISSICRELDAISNN
Retrocopy WEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPINLQKVDQFDPFTVPTISSICRELDAISNN

Parental  EEEKEENEAESDIKRRTRDYKKTSLAPYVKVFEQFLENLDKSRKGELLKKSDLQKDF
          EEEKEENEAESDIKRRTRDYKKTSLAPYVKVFEQFLENLDKSRKGELLKKSDLQKDF
Retrocopy EEEKEENEAESDIKRRTRDYKKTSLAPYVKVFEQFLENLDKSRKGELLKKSDLQKDF

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	0.11 RPM	7.51 RPM
SRP017611_kidney	0.10 RPM	2.43 RPM
SRP017611_liver	0.00 RPM	0.69 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1265 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1265 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1265 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265 ,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,