RetrogeneDB ID: retro_ecab_444

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:19662901..19663286(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000007662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDV3
• Ensembl ID: ENSECAG00000015689
• Aliases: None
• Description: CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]

Sequence

>retro_ecab_444
GGTGGTGGTGTAGAAAAATCTTCAGGTCCCTGCAATAAAACAGCTCCGGGGCAAGCACCTCTTGCTCCAGGAACTGTTAC
AGAAACCCCCAATCCGGCAATGACTAGTGATCTGTATAGGCCTCCCGGGGCGAGATTAACCACAACAAGGGAAAAAACAC
AAGGACCACCAGAAATAGACAGCGACACACAGTTCCCATCCCTGCAACCCACTGCCAAGCATGTGGGGAGCCGGAAGGAT
AAAGAGATGGAGAAGAGCTCTGAAAGTAGTCAGACACGGAATGAGACATAGGGATGAGCTTTCAAAAAGCCAGGCCCTTA
AACTGCAGCTAGACAACCGATGTGCTGTGCTGGAAGGTCAGAGAAGCAGCCGCGCACAGTCCAGT

Alignment

ORF - retro_ecab_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGVEKSSGPWNKTAPVQAPPAPGIVTETPEPAMTSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQS
          GGGVEKSSGP.NKTAP.QAP.APG.VTETP.PAMTS..YRPPGARLTTTR...QGPPEI.SDTQFPSLQ.
Retrocopy GGGVEKSSGPCNKTAPGQAPLAPGTVTETPNPAMTSDLYRPPGARLTTTREKTQGPPEIDSDTQFPSLQP

Parental  TAKHVESRKDKGMQKSFE-VVRHRTRRRDEVSGSQAPTLQLDNRCAVLGGQRSSCAQSS
          TAKHV.SRKDK.M.KS.E.VVRH..R.RDE.S.SQA..LQLDNRCAVL.GQRSS.AQSS
Retrocopy TAKHVGSRKDKEMEKSSE>VVRHGMRHRDELSKSQALKLQLDNRCAVLEGQRSSRAQSS

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
SRP021940_articular_cartilage	0.00 RPM	11.45 RPM
SRP021940_cerebellum	0.00 RPM	12.72 RPM
SRP021940_embryo	0.13 RPM	24.55 RPM
SRP021940_placental_villous	0.00 RPM	15.64 RPM
SRP021940_synovial_membrane	0.00 RPM	17.73 RPM
SRP021940_testis	0.06 RPM	73.28 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_444 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_444 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444 , retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Nomascus leucogenys	ENSNLEG00000003470	1 retrocopy	retro_nleu_1181,
Oryctolagus cuniculus	ENSOCUG00000012748	1 retrocopy	retro_ocun_1106,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,