RetrogeneDB ID: retro_ecab_97

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 27:22708127..22709048(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006030
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000005805
• Aliases: None
• Description: None

Sequence

>retro_ecab_97
ATGGACCAGCAACTGAAGAAAAGGGCAAAGACACAAGACGGGAAAGGCCTGGATAGAAGAGCCATCGTCGCTGGGGATAA
GCCACAGCGAGCCCAGGCCAGCCCAGCCCGGCAGGAATCTCTCGACATGACGTGGGCCTTAGGTGGTGAAGATGTGTACT
GTGAGACTTGCCATCAGCTTGTTGGAGAGGATTCCTTCTGCGACTGTTACATAGAATGCATAATAAGAGGTGAGTTTTCT
GAACCCATCCTGGAAGAAGACTTACTTCTTAAGTCCTTTGACTGCCTGACAGAAGGATCAGAACAAGACCTTTCTCAACA
GCTTCTTACCGCCAGCTCTCTTCTCGAATGTTCTCTGGAATACGTGAAAAAAGGGGCAAAACAAGACCTTCCCCAAGAGA
CTGTTGGCGAGAATTCACTTCTTGGGTATCCTGAGTACATGACAGGCAAGAGGCTTCCTCCTGGAGGAATATCCAGCGTT
GACTTACCAGATCCCCAACAGCTCTCAGAATCTGCTAGAAAGAAGCCAGGAAAAAATCAAGAATGTGATGCTCCAGAAAA
AATTGTTTGTCCTCAGAGCGGATGCACAAAAAAGTTGAAGAATAAGGCTTCCCTGAGAAAACATCTCCTCGTTCATGGGC
CCCGAGATCACGTATGTGCAGAATGTGGGAAAGCGTTCAATGAGAGCACAAAACTAAAAAGGCATTTCCTGGTTCATACT
GGAGAGAAGCCATTTCAGTGCACTTTCGAAGGGTGTGGAAAACGCTTTTCCCTGGACTTCAACTTGCGTACACATGTACG
CATCCACACCGGGGAGAAACGTTTTATGTGTCCCTTCGAAGGCTGTCACAAGAGGTTTATTCAGTCAAACAACATGAAAG
TTCACATCTTAACTCATGCAAAGACAAAAGGGAATCAATGA

Alignment

ORF - retro_ecab_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 90.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKGCTKMFRD
          ....GENS...Y.EYMTGK.LPPGGI...DL.DP.QL.E.AR.KP.K..E.DAP..I.CP..GCTK....
Retrocopy QETVGENSLLGYPEYMTGKRLPPGGISSVDLPDPQQLSESARKKPGKNQECDAPEKIVCPQSGCTKKLKN

Parental  NSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG
          ....RKHL..HGPR.HVCAECGKAF.ES.KLKRH.LVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG
Retrocopy KASLRKHLLVHGPRDHVCAECGKAFNESTKLKRHFLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG

Parental  DRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          .....CPF.GC.K.F.QS.N.K.HILTHAK.K.NQ
Retrocopy EKRFMCPFEGCHKRFIQSNNMKVHILTHAKTKGNQ

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	22.20 RPM
SRP021940_cerebellum	0.00 RPM	23.27 RPM
SRP021940_embryo	0.08 RPM	28.74 RPM
SRP021940_placental_villous	6.30 RPM	32.76 RPM
SRP021940_synovial_membrane	0.00 RPM	22.51 RPM
SRP021940_testis	0.00 RPM	31.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_97 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_97 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_97 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_106
Pan troglodytes	retro_ptro_45
Gorilla gorilla	retro_ggor_190
Pongo abelii	retro_pabe_145

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97 ,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,