RetrogeneDB ID: retro_ocun_1573

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018701:6276475..6276810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSOCUG00000015489
• Aliases: None
• Description: cAMP-regulated phosphoprotein, 19kDa [Source:HGNC Symbol;Acc:16967]

Sequence

>retro_ocun_1573
TTGTCCCAGGAAGTCCCTGAGAGCCCCGGGGAGAAGCTGAAGGAAATGGAAGATAAAGTGACTAGTCCACAGAAAGCTGC
AGAAGCAAAATTAAAAGCGAGATACCCTCATCTGGGACAAAAGCCTGGAGGTTCAGATTTCTTAAGGAAAAACAACTGCA
CAAAGGGCAAAAATATTTTGATTCTGGGGATTACCATGTGGCCAAAACAAAAATGAAGAAAGAACAACGTCCTACTGCAG
CCCCGGATCAAAAGGTGGTTGCCGGTGACCGTATTCCCACTGCACGGGACCTTGCGCAACGGGCGCCGTGCCTTGTCGCC
AGCAAGCTGGCCGGC

Alignment

ORF - retro_ocun_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAEVPETASAEEQKEMEDKVTSPEKAEEAKLKARYPHLGQKPGGSD-FLR-KRLQKGQKYFDSGDYNMA
          .S.EVPE....E..KEMEDKVTSP.KA.EAKLKARYPHLGQKPGGSD.FL..K.L.KGQKYFDSGDY..A
Retrocopy LSQEVPESPG-EKLKEMEDKVTSPQKAAEAKLKARYPHLGQKPGGSD<FLKEKQLHKGQKYFDSGDYHVA

Parental  KAKMKNKQLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASKLAG
          K.KMK..Q.PTAAPD...V.GD.IPT..DL.QR.P.LVASKLAG
Retrocopy KTKMKKEQRPTAAPDQKVVAGDRIPTARDLAQRAPCLVASKLAG

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	56.68 RPM
SRP017611_kidney	0.00 RPM	18.45 RPM
SRP017611_liver	0.00 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1573 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1573 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011022	5 retrocopies	retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952, retro_btau_981,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Cavia porcellus	ENSCPOG00000011228	1 retrocopy	retro_cpor_1148,
Dasypus novemcinctus	ENSDNOG00000004474	9 retrocopies	retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Echinops telfairi	ENSETEG00000015550	1 retrocopy	retro_etel_585,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Nomascus leucogenys	ENSNLEG00000006551	2 retrocopies	retro_nleu_2533, retro_nleu_2884,
Oryctolagus cuniculus	ENSOCUG00000003267	3 retrocopies	retro_ocun_296, retro_ocun_396, retro_ocun_722,
Oryctolagus cuniculus	ENSOCUG00000015489	10 retrocopies	retro_ocun_1182, retro_ocun_1297, retro_ocun_1398, retro_ocun_1573 , retro_ocun_1731, retro_ocun_1768, retro_ocun_310, retro_ocun_473, retro_ocun_479, retro_ocun_698,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Sus scrofa	ENSSSCG00000004618	1 retrocopy	retro_sscr_603,
Tursiops truncatus	ENSTTRG00000004804	1 retrocopy	retro_ttru_172,