RetrogeneDB ID: retro_ecab_1081

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:72739564..72739902(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSECAG00000015558
• Aliases: None
• Description: U2 small nuclear RNA auxiliary factor 1 [Source:HGNC Symbol;Acc:12453]

Sequence

>retro_ecab_1081
TTGCACTGTATGGTGTGCTATGTTGAAATGCAGGAACACTATGATGAATTTTTTGAAGAGGTTTTTATAGAAATGGAGAA
GTATCGTTAAGTTGAGGAGATGAACGTCTGTGATAACCTTGGAGATCACCTAGTTGGAGACGTGTATGTCAAGTTTCGCC
ATGAAGAAGATGCAGAAAATGTTGTAATTGACTTAAATAGCTGTTGGTTTAATGGACAGCGATCCGTGCTGAGCTCTCCC
CTGTGACCGACTTCAGAGATGCCTGCTGCTCACAGTATGAAATTGGAGTGTGTACACAAGGAGGCTTCTGCAACTTCCTG
CATTTGAAGCCCATTTCT

Alignment

ORF - retro_ecab_1081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 50.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW
          L.C.V..VEMQEHYDEFFEEVF.EME.KY..VEEMNVCDNLGDHLVG.VYVKFR.EEDAE..VIDLN..W
Retrocopy LHCMVCYVEMQEHYDEFFEEVFIEME-KYR*VEEMNVCDNLGDHLVGDVYVKFRHEEDAENVVIDLNSCW

Parental  FNGQ-PIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPIS
          FNGQ..I.AELSPVTDFR.ACC.QYE.G.CT.GGFCNF.HLKPIS
Retrocopy FNGQ<AIRAELSPVTDFRDACCSQYEIGVCTQGGFCNFLHLKPIS

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	25.80 RPM
SRP021940_cerebellum	0.00 RPM	40.92 RPM
SRP021940_embryo	0.05 RPM	65.77 RPM
SRP021940_placental_villous	0.00 RPM	40.46 RPM
SRP021940_synovial_membrane	0.00 RPM	35.19 RPM
SRP021940_testis	0.06 RPM	82.81 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1081 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1081 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081 ,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227, retro_pabe_703,