RetrogeneDB ID: retro_ocun_1296

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:32649114..32650066(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSOCUG00000006455
• Aliases: None
• Description: COP9 signalosome subunit 2 [Source:HGNC Symbol;Acc:30747]

Sequence

>retro_ocun_1296
CAGATGGATTAACTGCAGGAATTTTATGAAACAATAGTGGAAGCTTTGAAAGATGCTAAGAATGATAGACTGTGGTTTAA
GACAAACACAAAGCTTGGAAAATTGTATTTAGAATGAGGGGAATATGGAAAGCTTCAAAAAATTTTACGCCAGTTACACC
AATCCTGCCAGACTGATAATGAAGATGACCTGAAAAAAAGTACACAATTATTAGAAATATATGCTTTGGAAAATAAAACG
TACACAGCACAGAAAAGTAACAAAAAACTTAACGCACTCTATGAACAGTCCCTTCACATCAAGTCTGCCATCCTCATCTA
CTGATCCTGGGAGTCAGAGAATGTGGTGGTAAAATGCACTTGAGAGAAGGTGAATTTGAAAAGGCACATAGTGATTTTTT
TTAAAACCTTTAAGAATTACGATCAATCAGGAAATCCAAGACGAACCACTTGCTTAAAGTGTTTGGTCCTAGCAAACATG
TTAATGAAATCGAAATCAATCCATTTGACTTCAGGAGGCTAAGCTGTATAAAAATGATTCAGAAATTCTAGCAATGACAA
ATTTACTAAGTGCTTATCAGAATAATGACATCACTGAATTTGAAAAGATTCTGAAAACAAATCACAGCAACGTCATGGAT
GATCTTTTCATAAGAGAACACATTGAAGAGCTTTTGTGAAACATCAGAACACAAGTGCTCATAAAATTAATTAAACCTTA
CACAAGAATACATATTCCTTTTATTTCTAAGGAGTTAAACATAGATGTAGCTGATGTGGAGAGCTTGCTGATCCAGTGCA
TATTGGATAACACTATTCATGGCCGAATTGATCAAGTCAACCAACTTCTTGAACTGGATCATCAGAAGAGGAGAGGTGCA
CGATATATTGCACTAGACAAATGGGCCAATCAACTAAATTCTCTCAACCAGGCTATAGTCAGCAAACTAGCA

Alignment

ORF - retro_ocun_1296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLKKGTQ
          QMD.LQEFYET..EALKDAKNDRLWFKTNTKLGKLYLE..EYGKLQKILRQLHQSCQTD..EDDLKK.TQ
Retrocopy QMD*LQEFYETIVEALKDAKNDRLWFKTNTKLGKLYLE*GEYGKLQKILRQLHQSCQTDN-EDDLKKSTQ

Parental  LLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAI-PHPLIMGVIRECGGKMHLREGEFEKAHTDFF-EA
          LLEIYALE...YTAQK.NKKL.ALYEQSLHIKSAI.PH.LI.GV.RECGGKMHLREGEFEKAH.DFF...
Retrocopy LLEIYALENKTYTAQKSNKKLNALYEQSLHIKSAI<PHLLILGV-RECGGKMHLREGEFEKAHSDFF>KT

Parental  FKNYDESGSPRRTTCLKYLVLANMLMKSG-INPFDS-QEAKPYKNDPEILAMTNLVSAYQNNDITEFEKI
          FKNYD.SG.PRRTTCLK.LVLANMLMKS..INPFD..QEAK.YKND.EILAMTNL.SAYQNNDITEFEKI
Retrocopy FKNYDQSGNPRRTTCLKCLVLANMLMKSK<INPFDF<QEAKLYKNDSEILAMTNLLSAYQNNDITEFEKI

Parental  LKTNHSNIMDDPFIREHIEELLRNIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIH
          LKTNHSN.MDD.FIREHIEELL.NIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLL.QCILDNTIH
Retrocopy LKTNHSNVMDDLFIREHIEELL*NIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLLIQCILDNTIH

Parental  GRIDQVNQLLELDHQKRGGARYTALDKWTNQLNSLNQAVVSKLA
          GRIDQVNQLLELDHQKR.GARY.ALDKW.NQLNSLNQA.VSKLA
Retrocopy GRIDQVNQLLELDHQKRRGARYIALDKWANQLNSLNQAIVSKLA

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	0.06 RPM	50.44 RPM
SRP017611_kidney	0.10 RPM	46.42 RPM
SRP017611_liver	0.08 RPM	22.12 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1296 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1296 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160, retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296 ,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,