RetrogeneDB ID: retro_ecab_384

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:52947060..52947430(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C2orf76
• Ensembl ID: ENSECAG00000002063
• Aliases: None
• Description: chromosome 2 open reading frame 76 [Source:HGNC Symbol;Acc:27017]

Sequence

>retro_ecab_384
TCTGAAGAAGTGACCACTACAGGTCACCTCTTCGTTCTGTTGAACATCGCAATTTCAAATCTGTAATATATCATGGAGTT
AATTTGGACGAAACTGCAAAGGGATTTATAGTATTTCTGAAGCAAGATGTTTCTTTAAGATCAATCTGCCACCACCATTC
GGAAATTATAAATATGATAAACTAAAGATTATCCATCAAGCACATAAGTCAAAGACAAATGAACTTGTGTTGAGTTTGGG
AAACGATGGCACAACTCCCGTTATAAGAAAACAGTGCTTTGAAAGCAGCTGGAATTGCCAATGATACTGAAATTCATTCT
CCTGTGAAGAAGATTATACGAACTACAAAGCTAATCCCATTTCATCCTGG

Alignment

ORF - retro_ecab_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.31 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASEVTVTVRL-IRSFEHRNFRPVVYHGVNLDQTVKEFIVFLKQDIPLRT-SLPPPFRNYKYDKLKIIHQA
          ..EVT.T..L..RS.EHRNF..V.YHGVNLD.T.K.FIVFLKQD..LR...LPPPF.NYKYDKLKIIHQA
Retrocopy SEEVTTTGHL<LRSVEHRNFKSVIYHGVNLDETAKGFIVFLKQDVSLRS<NLPPPFGNYKYDKLKIIHQA

Parental  HKSKTNELVLSLEDDD-RLLLKEDGTLQAAGIANETEI-AFFCEEDYKNFKANPVSSW
          HKSKTNELVLSL..D...L.L.E...L.AAGIAN.TEI..F.CEEDY.N.KANP.SSW
Retrocopy HKSKTNELVLSLGNDG>QLPL*ENSALKAAGIANDTEI<SFSCEEDYTNYKANPISSW

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	0.30 RPM
SRP021940_cerebellum	0.00 RPM	0.62 RPM
SRP021940_embryo	0.00 RPM	1.38 RPM
SRP021940_placental_villous	0.00 RPM	0.29 RPM
SRP021940_synovial_membrane	0.00 RPM	0.38 RPM
SRP021940_testis	0.00 RPM	3.07 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_384 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_384 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_965
Canis familiaris	retro_cfam_1119

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008507	2 retrocopies	retro_amel_1062, retro_amel_1693,
Bos taurus	ENSBTAG00000010599	1 retrocopy	retro_btau_965,
Canis familiaris	ENSCAFG00000004896	2 retrocopies	retro_cfam_1119, retro_cfam_1727,
Equus caballus	ENSECAG00000002063	1 retrocopy	retro_ecab_384 ,
Myotis lucifugus	ENSMLUG00000004031	1 retrocopy	retro_mluc_1204,
Mustela putorius furo	ENSMPUG00000000943	1 retrocopy	retro_mputfur_726,
Mus musculus	ENSMUSG00000026388	1 retrocopy	retro_mmus_947,
Pteropus vampyrus	ENSPVAG00000011615	1 retrocopy	retro_pvam_337,
Sus scrofa	ENSSSCG00000015718	1 retrocopy	retro_sscr_311,