RetrogeneDB ID: retro_ocun_1469

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:25235832..25236365(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD2L1
• Ensembl ID: ENSOCUG00000008243
• Aliases: None
• Description: MAD2 mitotic arrest deficient-like 1 (yeast) [Source:HGNC Symbol;Acc:6763]

Sequence

>retro_ocun_1469
CAGCCTGCTGGGGAGCATGGTATCACCCTGCACTGGAGCACTGACTTCCCCGTGACCAGGTTCTGTTCATTTGGCATCAG
TAGCATTCTCTACCAGCGTTGCATACATCTGTCTGAAAGCTTCACTCGAGTGCAGAAATGTGGACTCACTTTGCTTGACA
CTGCTTCTCCTGAGCTCATAAAATACCCAAGTAATGTGGTGGAATAACTAAAAGATGGGTTATACAGGTATTCAATTTAG
AAACTGGTAAGAGTCATCTCAAATATTGAAAGCGGTGAGGGCCCTGAAAGACAGCAGTTTGATATGGAGTGTGACAAGAC
TGCAAAAAGATGACAGAGCTCCCAGAGAAGAGTCTCAAAACATTGTCCGAGATGAAATCCGCTCAGTGATCAGATGGGTC
ACAGCTTCCATGCCATGTCTGCCACTGTTAGAAGCGCCATGTTTTGTCGATCTATTGATTTACACAAGATTTGGATGCTC
TTGAAAAATGGCAAGAGCAGGGCCCACACTTCATCACCAATTCTGAGGAAGTC

Alignment

ORF - retro_ocun_1469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.85 %
• Parental protein coverage: 86.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLAREQGITLRGSAEI-VAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDPELIKYLNNVVEQL
          Q.A.E.GITL..S....V..F.SFGI.SILYQR.I..SE.FTRVQK.GLTLL.T..PELIKY..NVVE.L
Retrocopy QPAGEHGITLHWSTDFPVTRFCSFGISSILYQRCIHLSESFTRVQKCGLTLLDTASPELIKYPSNVVE*L

Parental  KDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTA-KDDSAPREKSQKVIQDEIRSVIRQITATVTF
          KD.LY..S..KLV.VISNIESGE..ER.QFD.ECDKTA.KDD.APRE.SQ....DEIRSVIR..TA....
Retrocopy KDGLYRYSI*KLVRVISNIESGEGPERQQFDMECDKTA>KDDRAPREESQNIVRDEIRSVIRWVTASMPC

Parental  LPLLEVSCSFDLLIYT-DKDLVVPEKWEESGPQFITNSEEV
          LPLLE..C..DLLIYT.D.D....EKW.E.GP.FITNSEEV
Retrocopy LPLLEAPCFVDLLIYT>DLDAL--EKWQEQGPHFITNSEEV

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	0.00 RPM	4.53 RPM
SRP017611_kidney	0.00 RPM	2.84 RPM
SRP017611_liver	0.00 RPM	0.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1469 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1469 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012813	2 retrocopies	retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus	ENSDNOG00000013456	1 retrocopy	retro_dnov_1348,
Erinaceus europaeus	ENSEEUG00000009629	1 retrocopy	retro_eeur_446,
Echinops telfairi	ENSETEG00000015756	1 retrocopy	retro_etel_724,
Gorilla gorilla	ENSGGOG00000002516	1 retrocopy	retro_ggor_1281,
Loxodonta africana	ENSLAFG00000029619	1 retrocopy	retro_lafr_1138,
Myotis lucifugus	ENSMLUG00000011092	8 retrocopies	retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta	ENSMMUG00000004875	2 retrocopies	retro_mmul_1292, retro_mmul_1701,
Mus musculus	ENSMUSG00000029910	2 retrocopies	retro_mmus_1684, retro_mmus_2573,
Oryctolagus cuniculus	ENSOCUG00000008243	4 retrocopies	retro_ocun_1424, retro_ocun_1469 , retro_ocun_1486, retro_ocun_752,
Otolemur garnettii	ENSOGAG00000004054	1 retrocopy	retro_ogar_199,
Ictidomys tridecemlineatus	ENSSTOG00000025410	2 retrocopies	retro_itri_1592, retro_itri_327,
Tupaia belangeri	ENSTBEG00000011065	3 retrocopies	retro_tbel_4460, retro_tbel_4666, retro_tbel_664,