RetrogeneDB ID: retro_ecab_311

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:44635505..44635757(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSECAG00000019174
• Aliases: None
• Description: frataxin [Source:HGNC Symbol;Acc:3951]

Sequence

>retro_ecab_311
TTTGTTGAAAACCTTGCAAACAAACATTACAAATTTAATCACTGAGATGTCTCATTTGGGAGTAGCATTTTAGTAATTAA
GCTGGGTGGAGATATAGGAGTTTACAGGACCAACAAGCAGACCCCAAATAAGCAAATCTGGTTGTCTTCTTCATCCAGTG
GTCCCCGGCATTATGATTCGAATGGGAAAAACTCGGTGTATTCACACGACAGCATACCCCTCCATGAAGTGCTGTCCACA
GAGCTGACTGAA

Alignment

ORF - retro_ecab_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.48 %
• Parental protein coverage: 54.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FFEDLADKPYTFEDYDVSFGSGVLTIKMGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHD
          F.E.LA.K.Y.F...DVSFGS..L.IK.GGD.G.Y..NKQTPNKQIWLSS.SSGP..YD..GKN.VYSHD
Retrocopy FVENLANKHYKFNH*DVSFGSSILVIKLGGDIGVYRTNKQTPNKQIWLSSSSSGPRHYDSNGKNSVYSHD

Parental  GVSLHELLAAELTK
          ...LHE.L..ELT.
Retrocopy SIPLHEVLSTELTE

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	3.31 RPM
SRP021940_cerebellum	0.00 RPM	16.15 RPM
SRP021940_embryo	0.00 RPM	12.91 RPM
SRP021940_placental_villous	0.00 RPM	4.96 RPM
SRP021940_synovial_membrane	0.00 RPM	6.53 RPM
SRP021940_testis	0.00 RPM	5.44 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_311 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_311 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2203
Macaca mulatta	retro_mmul_2038

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939, retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311 ,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203, retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175, retro_ttru_546, retro_ttru_831,