RetrogeneDB ID: retro_ecab_740

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:57378401..57379624(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSECAG00000013041
• Aliases: None
• Description: eukaryotic translation termination factor 1 [Source:HGNC Symbol;Acc:3477]

Sequence

>retro_ecab_740
AATGGCACAAGCATGATATCATTGATCATTCCTCCCAAAGACCAGATTTCAAGAGTGGCAAAAATGTTAGCAGATGAGTT
TGGAAGTGCATCTAACATTAAATCACGTGTAAACCGCCTTTCAGTCTTGGGAGCCATTACATCTGTACAGCAAAGACTCA
AACGTTGTAACAAAGTACCTCCAAATGGACTGGTTGTTTACTGTGGTACAATTGTAACAGAAGAAGGAAAGGAAAAGAAA
GTCAACATTGACTTTGAACCTTTCAAACCAGTTAATACGTCGTTGTATTTGTGCGACAACAAATTCCATACAGAGGCTCT
TACAGCACTACTTTCAGATGATAGCAAGTTTGGCTTCATTGTAATAGATGGTAGTGGTGCACTTTTTGGCACACTCCAAG
GAAAGACAAGAGAAGTCCTGCACAAATTCACTGTGGATCTCCCAAAGAAACATGGTAGAGGAGGTCAATCAGCCTTGCGT
TTTGCCTGTTTAAGAATGGAAAAGTGACATAACTATGTTTGGAAAGTAGCTGAGACTGCTGTACAGCTCATTATTTCAGG
GGACAAAGTAAATGTGGCTGGTCTCGTTTTAGCTGGATCAGCTGACTTTAAAACTGAACTAAGTCAATCTGATATGTTTG
ATCAGAGGTTGCAATCAAAAGTTTTAAAATTAGTTGATATATCCTATGGTGGTGAAAATGGATTCAACCAAGCTATTGAG
TTATCTACTGAAGTCCTGTCCAACGTGAATTCATTCAAGAGAAGAAATTAATAGGGCGGTACTTTGATGAAATCAGCCAG
GACACGGGCAAGTACTGTTTTGGAGTTGAAGATACACTAAAGGCTTTAGAAATGGGAGCTGTAGAGATCCTAATAGTCTA
TGAAAATCTGCGTATAATGAGATATGTTCTTCATTGCCAAGGCACGGAAGAGGAGAAAATTCTCTACCTAACTCCAGAAC
AAGAGAAGGATAAATCTCATTTCACAGACAAAGAGACAGGACAAGAACATGAGCTGATTGAGAGCATGCCCCTGCTGGAA
TGGTTTGCTAACAACTATAAAAAATTTGAAGCTACGTTGGAAATTGTCACTGATAAGTCACAAGAAGGATCCCAGTTTGT
GAAAGGATTTGGTGGAATTGGAGGTATCTTGCGGTACCGAGTAGATTTCCAGGGAATGGAATACCAAGGAGGAGACGATG
AATTTTTTGACCTTGATGACTAC

Alignment

ORF - retro_ecab_740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGT
          NGTSMISLIIPPKDQISRVAKMLADEFG.ASNIKSRVNRLSVLGAITSVQQRLK..NKVPPNGLVVYCGT
Retrocopy NGTSMISLIIPPKDQISRVAKMLADEFGSASNIKSRVNRLSVLGAITSVQQRLKRCNKVPPNGLVVYCGT

Parental  IVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVL
          IVTEEGKEKKVNIDFEPFKP.NTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQG.TREVL
Retrocopy IVTEEGKEKKVNIDFEPFKPVNTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGKTREVL

Parental  HKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQS
          HKFTVDLPKKHGRGGQSALRFA.LRMEK.HNYV.KVAETAVQL.ISGDKVNVAGLVLAGSADFKTELSQS
Retrocopy HKFTVDLPKKHGRGGQSALRFACLRMEK*HNYVWKVAETAVQLIISGDKVNVAGLVLAGSADFKTELSQS

Parental  DMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNV-KFIQEKKLIGRYFDEISQDTGKYCFGVEDT
          DMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNV..FIQEKKLIGRYFDEISQDTGKYCFGVEDT
Retrocopy DMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNV<EFIQEKKLIGRYFDEISQDTGKYCFGVEDT

Parental  LKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWF
          LKALEMGAVEILIVYENL.IMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWF
Retrocopy LKALEMGAVEILIVYENLRIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWF

Parental  ANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQGMEYQGGDDEFFDLDDY
          ANNYKKF.ATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQGMEYQGGDDEFFDLDDY
Retrocopy ANNYKKFEATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQGMEYQGGDDEFFDLDDY

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	0.71 RPM	12.99 RPM
SRP021940_cerebellum	0.36 RPM	10.02 RPM
SRP021940_embryo	1.10 RPM	15.16 RPM
SRP021940_placental_villous	1.25 RPM	30.36 RPM
SRP021940_synovial_membrane	0.60 RPM	12.55 RPM
SRP021940_testis	0.51 RPM	16.43 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_740 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740 ,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,