RetrogeneDB ID: retro_ecab_267

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:44698131..44698578(-)
• Located in intron of: ENSECAG00000006437

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG1
• Ensembl ID: ENSECAG00000017942
• Aliases: None
• Description: BCL2-associated athanogene [Source:HGNC Symbol;Acc:937]

Sequence

>retro_ecab_267
GCCCACAGCAAGGTGATGGGAGGACCAGGCTCAGAGTGAACATCACCCACAGTGAGAAGCACGACCTTCACATCACCCCA
CAGCAGGGCTGCAGTGAACTGATTCACCAAGGCCTGGCCTGCCTTGCTGAAGAGACAATAGGGGTTCTGTCACCTTTCTA
GAAACCAATCGTTAAGGGGAGATCCTTTAAGGCTATGGAGCAGCCATTGTCAGGACATGGAATGCAGAATGGTGTAACTG
GGACCTAGAATGGTCCAGAGGAAAAGTTTGACTTAAACAAGTTGAACGATTTGGAGAAGTTTGTGGAGAAGACAGCTGAC
CAATGGGAGGGGTGAATTAAGAGCTCATGGTTCAGCAGGATTTCCTGGCCAAGGATTTGTAGTCCGAAACTCTCTGCAAA
CTTGATAGGAGAGGAAAGCAACAACTGAACAATTGGAGGAGATATTG

Alignment

ORF - retro_ecab_267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.35 %
• Parental protein coverage: 68.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARSEEMAAAG-LSVTVTHSNEKHDLHVTPQEGCSEPIVQDLAQVVEEATGVPLPFQKLIFKGKSLKEMET
          A.S..M...G.L.V..THS.EKHDLH.TPQ.GCSE.I.Q.LA...EE..GV..PF.K.I.KG.S.K.ME.
Retrocopy AHSKVMGGPG<LRVNITHS-EKHDLHITPQQGCSELIHQGLACLAEETIGVLSPF*KPIVKGRSFKAMEQ

Parental  PLSALGIQNGCRVMLIGKKNSPEEEVELKKLKGLERSVEKIADQLE-ELNKELTGIQQGFLAKDLQAEAL
          PLS..G.QNG......G..N.PEE...L.KL..LE..VEK.ADQ.E...N.EL...QQ.FLAKDL..E.L
Retrocopy PLSGHGMQNG----VTGT*NGPEEKFDLNKLNDLEKFVEKTADQWE<GVN*ELM-VQQDFLAKDL*SETL

Parental  CRLDRK-VKATIEQFMKIL
          C.LDR...KAT.EQ...IL
Retrocopy CKLDRR<RKATTEQLEEIL

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	39.25 RPM
SRP021940_cerebellum	0.00 RPM	47.41 RPM
SRP021940_embryo	0.05 RPM	28.79 RPM
SRP021940_placental_villous	0.05 RPM	26.36 RPM
SRP021940_synovial_membrane	0.00 RPM	52.76 RPM
SRP021940_testis	0.00 RPM	129.55 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_267 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_267 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017845	1 retrocopy	retro_btau_901,
Choloepus hoffmanni	ENSCHOG00000012656	1 retrocopy	retro_chof_2328,
Callithrix jacchus	ENSCJAG00000008074	1 retrocopy	retro_cjac_4052,
Equus caballus	ENSECAG00000017942	1 retrocopy	retro_ecab_267 ,
Homo sapiens	ENSG00000107262	1 retrocopy	retro_hsap_4673,
Gorilla gorilla	ENSGGOG00000016534	1 retrocopy	retro_ggor_2899,
Macaca mulatta	ENSMMUG00000020148	1 retrocopy	retro_mmul_2487,
Nomascus leucogenys	ENSNLEG00000005204	1 retrocopy	retro_nleu_2165,
Oryctolagus cuniculus	ENSOCUG00000008945	1 retrocopy	retro_ocun_481,
Pongo abelii	ENSPPYG00000019138	1 retrocopy	retro_pabe_3630,
Pan troglodytes	ENSPTRG00000020856	1 retrocopy	retro_ptro_3105,
Tursiops truncatus	ENSTTRG00000010573	2 retrocopies	retro_ttru_252, retro_ttru_946,