RetrogeneDB ID: retro_ecab_726

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:75220458..75221167(+)
• 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_726
GTACACCAGGATTTCATTTTCAAGATGGACAGCCCATCAGACTCAGCTATGGTTTCACGTCGCACACCACAGGCTTGTGC
CAGGTCACCGTCTCCCCATACCAGTAGTTCAAGAAAACAACCTATGAGTGCAACACTTAGAGAACGATTAAGGAAAACCA
GATCTTCATTTAATTCCTGTTACAGTATGGTAAAACGTCTCAAAGTAGAGAATGAAGATGATCAGAACCTTTCAGAGAAA
CCAGCAACTTCAGTAGAAGAAAACCGTGTGGAATTTCGAGAAGATTTTAAACACAGACAGTGAATTTGAAGAAAATACGT
ATTTGAAAAATACCTTCGAGAATATCAATGCATGTGAATCTGATTCACTCGATGCTGGGTCATGCAGTGAGGATCTCCAA
AATGACTTTGTGAATGAGAATCTTCCCCAAAAAGGATTAAATGAAGAAAAAGCAAAATTGGTGAAGCAGATTCAGGAGAA
AGAGGACCTTCTTCAGAGGCTGAAACTAGTCAAAATGTACAGATCAAAGAATGACCTATCTCAGTTACATTGTTAATAAA
GAAGTGGAGAAGCTGTAGCCAGCTGTTGCTTTACGAGTTACAGTCAGCTGTCCGAGGAAAACAAGAAACTCAGCCTTACT
CAGTTGATAGACTACTATGGCTTAGATGATAAATTGCTACCCTATAACAGAAATGAAGAAGAATTTATA

Alignment

ORF - retro_ecab_726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 97.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VNQDFIFKMESPSDSAVISPGTPQACARPPSPHTSSSRKQPMSATLRERLRKTRSSFNSCYSVVKRLKVE
          V.QDFIFKM.SPSDSA..S..TPQACAR.PSPHTSSSRKQPMSATLRERLRKTRSSFNSCYS.VKRLKV.
Retrocopy VHQDFIFKMDSPSDSAMVSRRTPQACARSPSPHTSSSRKQPMSATLRERLRKTRSSFNSCYSMVKRLKV-

Parental  NEGDDQNFSEKPPTSVEENS-VEFREDVKRIDSEFEENTSLKNTFKDISACESESLHAGSCSEDLQNDFV
          .E..D.......P....E...V...E.....DSEFEENT.LKNTF..I.ACES.SL.AGSCSEDLQNDFV
Retrocopy -ENEDDQNLSEKPATSVEEN>VWNFEKILNTDSEFEENTYLKNTFENINACESDSLDAGSCSEDLQNDFV

Parental  NEDLPREGLNEEKAKLVKQIQEKEDLLRRLKLVKMYRSKNDLSQLQ-LLIKRWRSCSQLLLCELQSAL-S
          NE.LP..GLNEEKAKLVKQIQEKEDLL.RLKLVKMYRSKNDLSQL..LLIK.WRSCSQLLL.ELQSA...
Retrocopy NENLPQKGLNEEKAKLVKQIQEKEDLLQRLKLVKMYRSKNDLSQLH<LLIKKWRSCSQLLLYELQSAV>E

Parental  EENKKLSLTQLIDYYGLDDKLLHYNRNEEEFI
          E..K.LSLTQLIDYYGLDDKLL.YNRNEEEFI
Retrocopy ENKK-LSLTQLIDYYGLDDKLLPYNRNEEEFI

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	0.00 RPM	2.05 RPM
SRP021940_placental_villous	0.00 RPM	1.92 RPM
SRP021940_synovial_membrane	0.00 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_726 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_726 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,