RetrogeneDB ID: retro_ecab_887

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:68560003..68560641(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFR1
• Ensembl ID: ENSECAG00000005386
• Aliases: None
• Description: SWI5-dependent recombination repair 1 [Source:HGNC Symbol;Acc:29574]

Sequence

>retro_ecab_887
ATGGCAGAGGGAGAGGTGAACCAAGATTTCATTTCCAAAATGGAAAATCCATCAGACTCAGCTGTGACCTTACCCAGCAT
TCCACAGGCCTGTGCCCATCCACCACCTCCCCACACAAACAGTTCAAGAAAACAACCCATGTGTGCAATACTTAGAGAAC
AATTGAGGAAAATAAGGTCTTCATTTAACTCCCGTGACAGCATGGTAAAATGTCTTAAAGTAGAGAGTGAAGAAAACATT
CAGACCTTTTCAGAGAAACCTGCACCTTCAACAGAAAACTGTTTGGAATTTCAAGAAAATTTCAAACACATAGACAGTGA
ATTTGAAGAAAGTACATATTGAAAAATACCTTCAAGAATATCAACACCTGTGAATCTAAAGCACTTGAACCTGGGTCACG
CAGTGATGATCTCCAAAATGATTTTGTGAATAAGAATCTTGCCAAACAAGGATGAAATGAAGGAAAAGCGAAATTGGTGA
AGCAGGTTCAGGAGAAAGAAGACTTTCTTCGGAGGCTAAAAGTAGTCAAAATGTGTAGATCAAAGAATGACCTGTCTCAG
GTACCGTTGTTAACACGGAAGTGGAGAAGCTGTTACGAGTCGCAGTGGGCTGTGTCTGAGCAGGACAAGAAACTGAGC

Alignment

ORF - retro_ecab_887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.44 %
• Parental protein coverage: 86.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEGEVNQDFIFKMESPSDSAVISPGTPQACARPPSPHTSSSRKQPMSATLRERLRKTRSSFNSCYSVVK
          MAEGEVNQDFI.KME.PSDSAV..P..PQACA.PP.PHT.SSRKQPM.A.LRE.LRK.RSSFNS..S.VK
Retrocopy MAEGEVNQDFISKMENPSDSAVTLPSIPQACAHPPPPHTNSSRKQPMCAILREQLRKIRSSFNSRDSMVK

Parental  RLKVENEGDDQNFSEKPPTSVEENSVEFREDVKRIDSEFEENT-SLKNTFKDISACESESLHAGSCSEDL
          .LKVE.E...Q.FSEKP..S..EN..EF.E..K.IDSEFEE.T..LKNTFK.I..CES..L..GS.S.DL
Retrocopy CLKVESEENIQTFSEKPAPST-ENCLEFQENFKHIDSEFEEST<ILKNTFKNINTCESKALEPGSRSDDL

Parental  QNDFVNEDLPREGLNEEKAKLVKQIQEKEDLLRRLKLVKMYRSKNDLSQLQLLIKRWRSC--SQLLLCEL
          QNDFVN..L...G.NE.KAKLVKQ.QEKED.LRRLK.VKM.RSKNDLSQ..LL...WRSC..SQ....E.
Retrocopy QNDFVNKNLAKQG*NEGKAKLVKQVQEKEDFLRRLKVVKMCRSKNDLSQVPLLTRKWRSCYESQWAVSEQ

Parental  QSALS
          ...LS
Retrocopy DKKLS

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	1.71 RPM
SRP021940_cerebellum	0.00 RPM	0.21 RPM
SRP021940_embryo	0.10 RPM	2.05 RPM
SRP021940_placental_villous	0.00 RPM	1.92 RPM
SRP021940_synovial_membrane	0.03 RPM	1.02 RPM
SRP021940_testis	0.00 RPM	1.47 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_887 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_887 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005386	2 retrocopies	retro_ecab_726, retro_ecab_887 ,
Echinops telfairi	ENSETEG00000015444	1 retrocopy	retro_etel_1418,
Gorilla gorilla	ENSGGOG00000025713	1 retrocopy	retro_ggor_3039,
Macaca mulatta	ENSMMUG00000015327	1 retrocopy	retro_mmul_2606,
Pteropus vampyrus	ENSPVAG00000004202	1 retrocopy	retro_pvam_742,