RetrogeneDB ID: retro_ecab_56

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:38069087..38069663(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004411
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000005085
• Aliases: None
• Description: None

Sequence

>retro_ecab_56
ATGACTACAGCTTGGGTTCTGGTGCTCATGACCGTGGTGCTGGGCTTGGCCACAGCTGGCCCTGTCCCCACTTCCAAGCC
CACCACAACGTGGAGGGGCTGCCACATGGGCAGGTTCCAATCTCTGTCGCCACGGGAGCTGGAAGCCTTTAAGAAAGCCA
AGGATGCCTTGGAAGAGTCGCTCCTGCAGAACGACTGGAGCTGCAGCTCTCGCCTCTTCCCCATGACCAGAGACCTGAGG
CTGCTGCAGGTGCGGGAGCGCCCGGTGGCCCTGGAGGCTGAGCTACACCTGACGCTGAAGGTCCTGAGGACTGCGGCTGA
TGCGTCCCTGGGCGTCGTCCTGGACCAGCCCCTTCACACGCTGCGCCACATCCACTCCAGGCTCCGGGCCTGTGTCCCGG
CTCAGCCCACAGCAGGCCCCAGACCCCGGAGCCGCCTCCACCACTGGCTGCACCGGCTCCAGGAGGCCACGAAGAAGGAG
TCCCAAGGCTGCCTTGAGGCCTCCGTCACATTCAACCTCTTCCGCCTCCTCACACGGGACCTGAAATGTGTTGCCAGCGG
AGACCTGTGCGTCTGA

Alignment

ORF - retro_ecab_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAVRVLVLVIAGLGLARAGPVPTSKPATTQRSCDIGRFKSLSPSELEAFKKAKDALENSL--ENWTCRS
          M....VLVL....LGLA.AGPVPTSKP.TT.R.C..GRF.SLSP.ELEAFKKAKDALE.SL....W.C.S
Retrocopy MTTAWVLVLMTVVLGLATAGPVPTSKPTTTWRGCHMGRFQSLSPRELEAFKKAKDALEESLLQNDWSCSS

Parental  PVFPTTWDLRQLQVWERPVALEAELALTLKILAMVADSSLADILDRPLHTLRHIHSELQACVPARPTAGP
          ..FP.T.DLR.LQV.ERPVALEAEL.LTLK.L...AD.SL...LD.PLHTLRHIHS.L.ACVPA.PTAGP
Retrocopy RLFPMTRDLRLLQVRERPVALEAELHLTLKVLRTAADASLGVVLDQPLHTLRHIHSRLRACVPAQPTAGP

Parental  GPRGRLHQWLRQLHEVQKK-SWGCLEASVTFNLFRLLTRDLNCVASGDLCL
          .PR.RLH.WL..L.E..KK.S.GCLEASVTFNLFRLLTRDL.CVASGDLC.
Retrocopy RPRSRLHHWLHRLQEATKKESQGCLEASVTFNLFRLLTRDLKCVASGDLCV

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	1.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_56 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_56 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_58

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008614	1 retrocopy	retro_amel_68,
Canis familiaris	ENSCAFG00000005582	1 retrocopy	retro_cfam_58,
Equus caballus	ENSECAG00000005085	1 retrocopy	retro_ecab_56 ,
Felis catus	ENSFCAG00000010737	1 retrocopy	retro_fcat_111,
Monodelphis domestica	ENSMODG00000023790	1 retrocopy	retro_mdom_1793,
Mustela putorius furo	ENSMPUG00000017733	1 retrocopy	retro_mputfur_164,