RetrogeneDB ID: retro_ecab_43

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:45732469..45733657(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001003
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000025090
• Aliases: None
• Description: None

Sequence

>retro_ecab_43
ATGTCAGAAGGAAACGCCGCGGGCGAGCCCAGCGCTCCGGGAGGGTCCCGACCTCTCGGGGCCCCGGGGGCTCATCGGAG
GCGGCCGGCGCCTCCCCTCACGCCGGGCCGCCTTCCCTCCATTTGCTCCAGGGACCTCACCCTCGGGGGAGTCAAGAAGA
AAACCTTCACCCCAAATATCATCAGTCGGAAGATCAAGGAAGAGCCTGAGGAAGAAGTAACCATCAAGAAGGAGAAGCCT
GAAAGGGATAGAGACCGACAGCGAGAGGGGCACGGGCGGGGCCGGGGTCGCCCAGAAGTGATCCAGTCCCACTCCGTCTT
TGAGCAGGGCCCCGCTGAAATGATGAAGAAAAAGGGGAACCGAGACAAGACAGTGGATGTCTCGGACATTGGGCCCTCTC
ACATCATCAACAGCAAAAAAGAGAAGAGGGAGACAGATGAAGAAACAAAACAGATCTTGCGCATGCTGGAGAAGGATGAT
TTCATCCATGACCCTGGGCTGAGGAATGACACTCGAAACATGCCTGTGCAGCTGCCGCTGGCTCACTCAGGATGGCTTTT
TAATAAAGAGAATGAAGAACCGGATGTTAAACCTTTGTTGGCTGGCCCCAAGGAAGAGGACGTGGAGGTGGATGTGCCTG
TTTTGAAGGTGAAAGAGGAGCCACGAGCCAAGGAGGAGGAGGCCAAGGTGAAGGCTCCCAGAGCAGCCGGAAAGACCCCG
GGCCTCCCGAAGGATGTCTCTGTGGCAGAGCTGCTCAGGGAGCTGAGCCTTGCCCAGGAGGAAGAGCTGCTGTTCCTCCA
GCTGCCGGACACGCTCCCTGGCCAGCCACCTACTCAGGACATCAAGCCTATCAAGACAGAGGTGCAGAGTGAGGATGGAC
AGACGGTGGTTATAAAGCGGGAGAAAGACCGGGAAGCCAGGCTGGCGGAGAATGCTTGTACCCTGGCTGACCTGTCAGAG
GGCCAGGTTGGCAAGTTGCTCATCCGCAGGTCGGGGAAGGTGCACCTCCTCCTGGGCAAGGTGACTCTGGATGTGACCGT
AGGGACCGCCTGCTCTTTCCTGCAGGAGCTGGTGTCTGTGGGCCTTGGAGACAGTAGGACAGGTGAAATGATAGTCCTGG
GACATGTAAATCACAAACTTGTGTGTTCCCCGGATTTTGAATCCCTCTTGGATCACAAACACCGGTAA

Alignment

ORF - retro_ecab_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGGPRPLLSGARGLIGRRPAPPLTPGRLPSIRSRDLTLGGVKKKTFTPNIISRKIKEEPKEEVTIKKEKR
          PGG.RPL..GA.G...RRPAPPLTPGRLPSI.SRDLTLGGVKKKTFTPNIISRKIKEEP.EEVTIKKEK.
Retrocopy PGGSRPL--GAPGAHRRRPAPPLTPGRLPSICSRDLTLGGVKKKTFTPNIISRKIKEEPEEEVTIKKEKP

Parental  ERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKGNWDKTVDVSDIGPSHIINIKKEKRETDEETK
          ERDRDRQREGHGRGRGRPEVIQSHS.FEQGPAEMMKKKGN.DKTVDVSDIGPSHIIN.KKEKRETDEETK
Retrocopy ERDRDRQREGHGRGRGRPEVIQSHSVFEQGPAEMMKKKGNRDKTVDVSDIGPSHIINSKKEKRETDEETK

Parental  QILRMLEKDDFIDDPGLRNDTRNMPVQLPLAHSGWLFKEESEEPDVKPSLAGPKEEDMEVDVPVVKVKEE
          QILRMLEKDDFI.DPGLRNDTRNMPVQLPLAHSGWLF..E.EEPDVKP.LAGPKEED.EVDVPV.KVKEE
Retrocopy QILRMLEKDDFIHDPGLRNDTRNMPVQLPLAHSGWLFNKENEEPDVKPLLAGPKEEDVEVDVPVLKVKEE

Parental  PRDEEEEAKVKAPPRAARKTPGLPKDVSVAELLRELSLAQEEELLFLQLPDTLPGQPPTQDIKPIKTEVQ
          PR..EEEAKVKA.PRAA.KTPGLPKDVSVAELLRELSLAQEEELLFLQLPDTLPGQPPTQDIKPIKTEVQ
Retrocopy PRAKEEEAKVKA-PRAAGKTPGLPKDVSVAELLRELSLAQEEELLFLQLPDTLPGQPPTQDIKPIKTEVQ

Parental  SEDGQMVVIKQEKDREARLAENACTLADLTEGQVGKLLIRRSGKVQLLLGKVTLDVTVGTACSFLQELVS
          SEDGQ.VVIK.EKDREARLAENACTLADL.EGQVGKLLIRRSGKV.LLLGKVTLDVTVGTACSFLQELVS
Retrocopy SEDGQTVVIKREKDREARLAENACTLADLSEGQVGKLLIRRSGKVHLLLGKVTLDVTVGTACSFLQELVS

Parental  VGLGDSRTGEMTVLGHVKHKLVCSPDFESLLDHKHR
          VGLGDSRTGEM.VLGHV.HKLVCSPDFESLLDHKHR
Retrocopy VGLGDSRTGEMIVLGHVNHKLVCSPDFESLLDHKHR

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	0.30 RPM	10.15 RPM
SRP021940_cerebellum	0.10 RPM	9.09 RPM
SRP021940_embryo	0.51 RPM	25.39 RPM
SRP021940_placental_villous	0.43 RPM	15.83 RPM
SRP021940_synovial_membrane	0.63 RPM	17.24 RPM
SRP021940_testis	0.32 RPM	18.03 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_43 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_43 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_43 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43 ,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,