RetrogeneDB ID: retro_ocun_498

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:41167973..41168698(+)
• Located in intron of: ENSOCUG00000004246

Retrocopy information

• Ensembl ID: ENSOCUG00000007537
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSOCUG00000017824
• Aliases: None
• Description: coiled-coil domain containing 59 [Source:HGNC Symbol;Acc:25005]

Sequence

>retro_ocun_498
ATGGCGCCGGTAAGGCCGGCGGCGAGGTGGCAGTTTGATGGTGTTGGAACGCGTGGCGAAGGGGTTTCTCCAGTTGGTTT
CAGGAAAAAGAACGGGAAACAGAGAACCTGGTGGCCTAGTCATACGCAGGGCTTCGCGGGGAGCGTTCGCCAGGGGCAAG
GCTTTGCATTTCGAAGAAAACTGAAGATTCAGCAAAATTACAAGAAGTTGCAACGGAGGGAAAAGAAGGCTCAGACATCG
CAAGAATCCCAGTTCACAGATCGATACCCAGATCATTTGAAACATCTCTATTTAGCTGAAGAGGAAAGGCTAAAGAAGCA
ACTAAGAAAAGCTGACCGACCGCTGTCAGAAAAGCAAGCTGATCAGCCTTTGCCTGAAGAACAGTATAGCACTGACCAGG
CCTTGTCTGAAGATCAGCATACTTTCCACCTCCTGAGCCGGAAGAACAGCATACCAGAACAGTAAACTCCATTACTGTTC
CAAAGAAAAATAAAAAGAAAACATCAAATCAGAAAGCACAAGAAGAATATGAACAGATACAAGCTGTGCGTGCCGCTAAG
AAACAAGAATTTGAGAGGAAAAAACAAGAGAGAGAAGCAGCTCAAAGGCTCTACAAAAAGAAGAAAATGGAAGTCTTCAA
AATATTGAGCAAAAAGACTAAAAAGGGCCAACCAAACTTGAATTTGCAAATGGAATATCTTCTTCAAAAAATACAAGAAA
AAAAT

Alignment

ORF - retro_ocun_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPVRPAARWQFDGVGTRGEGVSPVGFRKKNGKQRTWWPSHTQGFAGSVRQGQGFAFRRKLKIQQNYKKL
          MAPVRPAARWQFDGVGTRGEGVSPVGFRKKNGKQRTWWPSHTQGFAGSVRQGQGFAFRRKLKIQQNYKKL
Retrocopy MAPVRPAARWQFDGVGTRGEGVSPVGFRKKNGKQRTWWPSHTQGFAGSVRQGQGFAFRRKLKIQQNYKKL

Parental  QRREKKAQTSQESQFTDRYPDHLKHLYLAEEERLKKQLRKADRPLSEKQADQPLPEEQYSIDQALSEDQR
          QRREKKAQTSQESQFTDRYPDHLKHLYLAEEERLKKQLRKADRPLSEKQADQPLPEEQYS.DQALSEDQ.
Retrocopy QRREKKAQTSQESQFTDRYPDHLKHLYLAEEERLKKQLRKADRPLSEKQADQPLPEEQYSTDQALSEDQH

Parental  TVRL-PEPEEQHTRTESSITVPKKNKKKTSNQKAQEEYEQIQAVRAAKKQEFERRKQEREAAQRLYKKKK
          T..L.PEPEEQHTRT..SITVPKKNKKKTSNQKAQEEYEQIQAVRAAKKQEFER.KQEREAAQRLYKKKK
Retrocopy TFHL<PEPEEQHTRTVNSITVPKKNKKKTSNQKAQEEYEQIQAVRAAKKQEFERKKQEREAAQRLYKKKK

Parental  MEVFKILSKKTKKGQPNLNLQMEYLLQKIQEKN
          MEVFKILSKKTKKGQPNLNLQMEYLLQKIQEKN
Retrocopy MEVFKILSKKTKKGQPNLNLQMEYLLQKIQEKN

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	7.95 RPM
SRP017611_kidney	0.30 RPM	6.49 RPM
SRP017611_liver	0.00 RPM	2.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_498 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498 ,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,