RetrogeneDB ID: retro_ecab_13

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:34823126..34824221(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003698
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000017754
• Aliases: None
• Description: None

Sequence

>retro_ecab_13
ATGAGTTTGGCTGGGGGCCAGGCCCCCCGGAAGACCGCGGGGAACCGGCTTTCTGGGCTCCTGGAGGCAGAGGAGGAAGA
TGAGTTCTACCAGACGACTTATGGGGGTTTCACAGAGGAATCAGGAGATGATGAGTATCAAGGGGACCAGTCAGACACAG
AGGATGAGGTGGACTCTGACTTTGACATCGATGAAGGAGATGAACCATCCAGTGATGGAGAAGCAGAAGAGCCAAGAAGG
AAGCGCCGAGTAGTCACCAAAGCCTATAAGGAGCCTCTCAAGAGCTTAAGGCCTCGAAAGGTCAGCACCCCAGCTGGTAG
CTCTCAAAAGGCCAGAGAAGAGAAGGCACTGCTACCACTAGAACTACAAGATGATGGCTCTGACAGTCGGAAGTCCATGC
GTCAGTCTACAGCTGAGCATACAAGACAAACATTCCTTCGGGTACAGGAGAGGCAGGGCCAGTCACGGCGGCGAAAGGGG
CCCCACTGTGAGCGACCACTGACCCAGGAGGAGCTGCTCAGGGAGGCCAAGATCACAGAGGAGCTCAACTTACGTTCACT
GGAGACATATGAGCGGCTGGAGGCTGACAAAAAGAAGCAGGTTCACAAGAAGCGGAAGTGCCCTGGGCCCATAATCACGT
ATCATTCAGTGACAGTGCCGCTTGTTGGGGAGCCAGGCCCTAAAGAAGAGAATGTCGATGTAGAAGGGCTTGATCCTGCT
CCCACGGCTTCTGCACTGACTCCCCGTGCTGGGACTGGACCCATCATCCCTCCTGCTCGCTGCTCACGTACCTTCATCAC
TTTTAGTGATGATGCGACATTTGAAGAATGGTTTCCCCAGGGGCGGCCCCCAAAGGTCCCTGTTAGAGAGGTCTGCCCGG
TGACCCATCGGCCAGCCCTATACCGGGATCCTGTTACAGACATACCCTGCGCCACTGCTCGAGCCTTCAAGATCATCCGT
GAGGCCTACAAGAAGTACATCACTGCCCATGGACTGCCTCCCACTGCCTCAGCCCTGGGCCCTGGCCCGCCACCTCCTGA
GCCTCTCCCCGGCTCTGGGCCCCGAGCCTTGCGTCAGAAAATTGTCATCAAATGA

Alignment

ORF - retro_ecab_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLAGGRAPRKTAGNRLSGLLEAEEEDEFYQTTYGDRSEESGDDEYQGDQSDTEDEVDSDFDIDEGDEPS
          MSLAGG.APRKTAGNRLSGLLEAEEEDEFYQTTYG...EESGDDEYQGDQSDTEDEVDSDFDIDEGDEPS
Retrocopy MSLAGGQAPRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSDFDIDEGDEPS

Parental  SDGEAEEPRRKRRVVTKAYKEPLKSLRPRKVSTPAGSSQKAREEKALLPLELQDDGSDSRKSMRQSTAEH
          SDGEAEEPRRKRRVVTKAYKEPLKSLRPRKVSTPAGSSQKAREEKALLPLELQDDGSDSRKSMRQSTAEH
Retrocopy SDGEAEEPRRKRRVVTKAYKEPLKSLRPRKVSTPAGSSQKAREEKALLPLELQDDGSDSRKSMRQSTAEH

Parental  TRQTFLRVQERQGQSRRRKGPHCERPLTQEELLREAKITEELNLRSLETYERLEADKKKQVHKKRKCP-P
          TRQTFLRVQERQGQSRRRKGPHCERPLTQEELLREAKITEELNLRSLETYERLEADKKKQVHKKRKCP.P
Retrocopy TRQTFLRVQERQGQSRRRKGPHCERPLTQEELLREAKITEELNLRSLETYERLEADKKKQVHKKRKCPGP

Parental  IITYHSVTVPLVGEPGPKEENVDVEGLDPAPTASALTPRAGTGPIIPPARCSRTFITFSDDATFEEWFPQ
          IITYHSVTVPLVGEPGPKEENVDVEGLDPAPTASALTPRAGTGPIIPPARCSRTFITFSDDATFEEWFPQ
Retrocopy IITYHSVTVPLVGEPGPKEENVDVEGLDPAPTASALTPRAGTGPIIPPARCSRTFITFSDDATFEEWFPQ

Parental  GRPPKVPVREVCPVTHRPALYRDPVTDIPYATARAFKIIREAYKKYITAHGLPPTASALGPGPPPPEPLP
          GRPPKVPVREVCPVTHRPALYRDPVTDIP.ATARAFKIIREAYKKYITAHGLPPTASALGPGPPPPEPLP
Retrocopy GRPPKVPVREVCPVTHRPALYRDPVTDIPCATARAFKIIREAYKKYITAHGLPPTASALGPGPPPPEPLP

Parental  GSGPRALRQKIVIK
          GSGPRALRQKIVIK
Retrocopy GSGPRALRQKIVIK

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	0.47 RPM	2.60 RPM
SRP021940_cerebellum	1.77 RPM	4.83 RPM
SRP021940_embryo	4.04 RPM	9.77 RPM
SRP021940_placental_villous	0.91 RPM	4.14 RPM
SRP021940_synovial_membrane	1.48 RPM	3.79 RPM
SRP021940_testis	3.20 RPM	8.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_13 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_13 has 0 orthologous retrocopies within eutheria group .

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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	ENSAMEG00000000824	1 retrocopy	retro_amel_1768,
Canis familiaris	ENSCAFG00000012540	1 retrocopy	retro_cfam_807,
Equus caballus	ENSECAG00000017754	1 retrocopy	retro_ecab_13 ,
Echinops telfairi	ENSETEG00000004257	1 retrocopy	retro_etel_101,
Mustela putorius furo	ENSMPUG00000004027	1 retrocopy	retro_mputfur_1542,
Mus musculus	ENSMUSG00000008958	1 retrocopy	retro_mmus_1570,