RetrogeneDB ID: retro_ocun_1228

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:34822249..34822717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSOCUG00000022505
• Aliases: None
• Description: S-phase kinase-associated protein 1 [Source:HGNC Symbol;Acc:10899]

Sequence

>retro_ocun_1228
ATGCCTTCAATAAAGTTGCAGAGTTCTGATGGAGAGATTTTTGAAGTTGATGTAGAAATTGCCAAACAGTCTGTGACTAT
CAAGACCATGTTGGAAGATTTGGAGATGGATGATGAAGGAGATGATGACCCAGTTCCTCTACCAAATGTTAAAGCAGCAA
TATTAAAAAAGATCATTCAGTAGTGCACCCACCACAAGGATGACCCTCCTCCTCCTGAAGACGATGAGAACAAAGAAAAG
CGAACGGATGATATCCCTGTTTGGGACCAGGAATTCCTGAAAGTTGACCAAGGAACACTTTTTGAGCTTATTCTGGCTGC
AAACTACTTAGACATCAAAGATTTGCTGGACATTACATGCAAGACTGTTGTCAATATGATCAAGGGGAAGACTCCTGAGG
AGATTCGCAAGACCTTCAACATTAAGAATGACTTTACTGAAGCAGCAGCAGCCCAGGTACGCAGAGAA

Alignment

ORF - retro_ocun_1228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.95 %
• Parental protein coverage: 95.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPP
          MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDL.MDDEGDDDPVPLPNV.AAILKK.IQ.CTHHKDDPP
Retrocopy MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLEMDDEGDDDPVPLPNVKAAILKKIIQ*CTHHKDDPP

Parental  PPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFN
          PPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIK.LLD.TCKTV.NMIKGKTPEEIRKTFN
Retrocopy PPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKDLLDITCKTVVNMIKGKTPEEIRKTFN

Parental  IKNDFTEEEEAQVRKE
          IKNDFTE...AQVR.E
Retrocopy IKNDFTEAAAAQVRRE

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	0.55 RPM	217.39 RPM
SRP017611_kidney	0.20 RPM	136.83 RPM
SRP017611_liver	0.00 RPM	40.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1228 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1228 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017810	1 retrocopy	retro_amel_897,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Dasypus novemcinctus	ENSDNOG00000012999	9 retrocopies	retro_dnov_1216, retro_dnov_1338, retro_dnov_2433, retro_dnov_2526, retro_dnov_2647, retro_dnov_281, retro_dnov_286, retro_dnov_389, retro_dnov_776,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Felis catus	ENSFCAG00000031140	1 retrocopy	retro_fcat_653,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Oryctolagus cuniculus	ENSOCUG00000022505	10 retrocopies	retro_ocun_1119, retro_ocun_1228 , retro_ocun_1242, retro_ocun_1420, retro_ocun_1453, retro_ocun_1572, retro_ocun_1784, retro_ocun_397, retro_ocun_448, retro_ocun_553,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Vicugna pacos	ENSVPAG00000001583	1 retrocopy	retro_vpac_279,