RetrogeneDB ID: retro_ecab_975

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:63406411..63406627(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000003460
• Aliases: None
• Description: None

Sequence

>retro_ecab_975
CAAAGTTACTTTTTGGACAAATATGACCACGAGGCATTCGAGTACCAGCATGCCATGTTACCCGAGGATACAGCCAAGCT
GGTCTTTAAAATTCATTTAATGTCAGAATCTGAATGGAGGAATTTTAGCATTCAGTAGAGTCAGGGTTAGGGCCATTGTA
TGATTCATGAGCCAGAACCTCACATCTTGCTGTACCAGTATCCCCTGCCCAGGGAG

Alignment

ORF - retro_ecab_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 91.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFRRPLP
          Q.Y..DKYD.E.FEY.H.MLP.D.AKLV.K.HLMSESEWRN...Q.SQG..H.MIHEPEPHILL...PLP
Retrocopy QSYFLDKYDHEAFEYQHAMLPEDTAKLVFKIHLMSESEWRNFSIQ*SQG*GHCMIHEPEPHILLYQYPLP

Parental  KK
          ..
Retrocopy RE

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	1.36 RPM
SRP021940_cerebellum	0.00 RPM	7.27 RPM
SRP021940_embryo	0.00 RPM	19.54 RPM
SRP021940_placental_villous	0.00 RPM	6.93 RPM
SRP021940_synovial_membrane	0.00 RPM	5.79 RPM
SRP021940_testis	0.00 RPM	28.39 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_975 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_975 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033635	10 retrocopies	retro_cjac_13, retro_cjac_1441, retro_cjac_1478, retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Equus caballus	ENSECAG00000003460	1 retrocopy	retro_ecab_975 ,
Echinops telfairi	ENSETEG00000003337	4 retrocopies	retro_etel_1246, retro_etel_1938, retro_etel_239, retro_etel_497,
Felis catus	ENSFCAG00000001347	1 retrocopy	retro_fcat_1041,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Gorilla gorilla	ENSGGOG00000013419	4 retrocopies	retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Loxodonta africana	ENSLAFG00000032213	1 retrocopy	retro_lafr_243,
Mus musculus	ENSMUSG00000028044	1 retrocopy	retro_mmus_280,
Nomascus leucogenys	ENSNLEG00000011532	3 retrocopies	retro_nleu_1098, retro_nleu_2592, retro_nleu_411,
Oryctolagus cuniculus	ENSOCUG00000016204	2 retrocopies	retro_ocun_1389, retro_ocun_18,
Otolemur garnettii	ENSOGAG00000006384	10 retrocopies	retro_ogar_1673, retro_ogar_1703, retro_ogar_1713, retro_ogar_1983, retro_ogar_2317, retro_ogar_245, retro_ogar_3310, retro_ogar_450, retro_ogar_530, retro_ogar_877,
Pongo abelii	ENSPPYG00000000768	3 retrocopies	retro_pabe_1143, retro_pabe_3625, retro_pabe_717,
Pan troglodytes	ENSPTRG00000001398	4 retrocopies	retro_ptro_2769, retro_ptro_3100, retro_ptro_558, retro_ptro_944,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sorex araneus	ENSSARG00000012383	2 retrocopies	retro_sara_667, retro_sara_77,
Sus scrofa	ENSSSCG00000029737	1 retrocopy	retro_sscr_730,
Vicugna pacos	ENSVPAG00000012182	1 retrocopy	retro_vpac_532,