RetrogeneDB ID: retro_ocun_899

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:69322068..69323264(-)
• Located in intron of: ENSOCUG00000003236

Retrocopy information

• Ensembl ID: ENSOCUG00000004287
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPN1
• Ensembl ID: ENSOCUG00000011098
• Aliases: None
• Description: ribophorin I [Source:HGNC Symbol;Acc:10381]

Sequence

>retro_ocun_899
TATAGTCAGGATGCTTTTAAAGTACACTATGAGAACAACAGCCCTTTCCTGACCATCACCAGCATGACCCGCGTCATCGA
GGTCTCCCACTGGGGCAATAGCGCTGTGGAGGAAAACGCGGACTTGAAGCACACGGGGGCTGTGCTGAAGGGGCCCTTCT
CACGCTACGACTACCAGAGACAGCCCAACAGTCAGATCTCCTCCATCCGCTCCTTCAAGACCATCCTCCCTGCGGCTGCC
CAGGATGTTTACTACCGGGGTGAGATCAGCAACGTGTCCACCAGCCACCTCCTCATTTTGGATGACTCCGTAGAGATGGA
AATCTGGCCTCGCTTCCCTCTCTTTGGAGGGTGGAAGACACATTACATCGTTGGCTACAACCTCCCAAGCTATGAATACC
TCTATAATTTGGGCGATCAGTATGCACTGAAGATGAGATTTGTGGACCATGTGTTTGATGAGCAGGTGATAGATTCTCTG
ACTGTGAAGATCATTCTGCCTGAAGGAGCCAAGAATATCCAAGTTGATAGTCCTTATGAAATCAGCCGTGCCCCAGATGA
GCTGCACTACACTTACCTGGACACATTTGGCCGCCCTGTGATTGTTGCTTACAAGAAAAATCTGGTAGAACAGCACATCA
GGACATTGTGGCCCACTACACGTTCAACAAGGTGCTCGTGCTGCAGGAGCCCCTGCTGGTGGTAGCTGCCTTCTACATCC
TGTTCTTCACCGTCATCATCTATGTCTGTCTGGACTTTTCCATCACCAAGGATCCAGCTGCGGAAGCCAGAATGAAAGTG
GCTTGCATCACAGAGCAGGTCTTGACCCTGGTCAACAAGAGAATAGGCCTCTACCGTCACTTTGACGAGACCATTAATAG
GTACAAGCAATCTCGGGATGTCTCCACTCTGAACAGCGGCAAGAAGAGCCTGGAGACTGAACACAAGGCCTTGACCAGTG
AGATTGCTCTGCTGCAGTCCAGGCTGAAGACAGAGGGCTCTGATCTGTGCGACAGAGTGAGTGAAATGCAGAAGCTGGAC
GTGCAGGTCAAGGAGCTGGTGTTGAAGTCGGCGGTGGAGGCCGAGCGGCTGGTGGCCAGCAAGCTCAAGAAGGACACGTA
CATCGAGAATGAGAAGCTCATCTCTGGAAAGCGTCAGGAGCTGGTCACCAAGATCAACCACATCTTGGATGCTCTG

Alignment

ORF - retro_ocun_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.75 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YSQDAFKVHYENNSPFLTITSMTRVIEVSHWGNIAVEENVDLKHTGAVLKGPFSRYDYQRQPDSGISSIR
          YSQDAFKVHYENNSPFLTITSMTRVIEVSHWGN.AVEEN.DLKHTGAVLKGPFSRYDYQRQP.S.ISSIR
Retrocopy YSQDAFKVHYENNSPFLTITSMTRVIEVSHWGNSAVEENADLKHTGAVLKGPFSRYDYQRQPNSQISSIR

Parental  SFKTILPAAAQDVYYRDEIGNVSTSHLLILDDSVEMEIRPRFPLFGGWKTHYIVGYNLPSYEYLYNLGDQ
          SFKTILPAAAQDVYYR.EI.NVSTSHLLILDDSVEMEI.PRFPLFGGWKTHYIVGYNLPSYEYLYNLGDQ
Retrocopy SFKTILPAAAQDVYYRGEISNVSTSHLLILDDSVEMEIWPRFPLFGGWKTHYIVGYNLPSYEYLYNLGDQ

Parental  YALKMRFVDHVFDEQVIDSLTVKIILPEGAKNIQVDSPYEISRAPDELHYTYLDTFGRPVIVAYKKNLVE
          YALKMRFVDHVFDEQVIDSLTVKIILPEGAKNIQVDSPYEISRAPDELHYTYLDTFGRPVIVAYKKNLVE
Retrocopy YALKMRFVDHVFDEQVIDSLTVKIILPEGAKNIQVDSPYEISRAPDELHYTYLDTFGRPVIVAYKKNLVE

Parental  QHI-QDIVVHYTFNKVLMLQEPLLVVAAFYILFFTVIIYVRLDFSITKDPAAEARMKVACITEQVLTLVN
          QHI.QDIV.HYTFNKVL.LQEPLLVVAAFYILFFTVIIYV.LDFSITKDPAAEARMKVACITEQVLTLVN
Retrocopy QHI<QDIVAHYTFNKVLVLQEPLLVVAAFYILFFTVIIYVCLDFSITKDPAAEARMKVACITEQVLTLVN

Parental  KRIGLYRHFDETINRYKQSRDVSTLNSGKKSLETEHKALTSEIALLQSRLKTEGSDLCDRVSEMQKLDVQ
          KRIGLYRHFDETINRYKQSRDVSTLNSGKKSLETEHKALTSEIALLQSRLKTEGSDLCDRVSEMQKLDVQ
Retrocopy KRIGLYRHFDETINRYKQSRDVSTLNSGKKSLETEHKALTSEIALLQSRLKTEGSDLCDRVSEMQKLDVQ

Parental  VKELVLKSAVEAERLVAGKLKKDTYIENEKLISGKRQELVTKIDHILDAL
          VKELVLKSAVEAERLVA.KLKKDTYIENEKLISGKRQELVTKI.HILDAL
Retrocopy VKELVLKSAVEAERLVASKLKKDTYIENEKLISGKRQELVTKINHILDAL

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	5.19 RPM	104.69 RPM
SRP017611_kidney	0.41 RPM	193.49 RPM
SRP017611_liver	4.39 RPM	96.65 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_899 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_899 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005191	1 retrocopy	retro_btau_123,
Callithrix jacchus	ENSCJAG00000017529	1 retrocopy	retro_cjac_601,
Myotis lucifugus	ENSMLUG00000017213	1 retrocopy	retro_mluc_721,
Oryctolagus cuniculus	ENSOCUG00000011098	1 retrocopy	retro_ocun_899 ,