RetrogeneDB ID: retro_ecab_1085

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:80712714..80713314(+)
• Located in intron of: ENSECAG00000020186

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMMECR1L
• Ensembl ID: ENSECAG00000023095
• Aliases: None
• Description: AMMECR1-like [Source:HGNC Symbol;Acc:28658]

Sequence

>retro_ecab_1085
ATGGGAAAAAGACATCGTGTTTCTCCACTCAAGCCCAAGTTGGCAGAATGCTGTTGTGGGGTCAAGAAGCTTAAATTACC
TGGAAATGGAACACACAGTCACAGGAACCAGTCCACAACTGTCCCCGGCTCTAGTTCAGGACATTTTCAAAACCACAAGC
ACGTGGGTGGCAGCAGTGGTCAGGAGAATGTGTTGGACTTAACTCTGGGATCCAGAAATTCTCCCTATTATACAAATGAA
TCCCTCATCAGGAGCACTGAGCCCTCTCCTCGGGCCCAATGGAACTACCAACAACACCAAAAATTTGGTGGTGACTGCAG
AGATGTGCTGCTACTGCTTTGACATCTTCTATTGTCACCTTTATGGCTTCCCACAGTCACAACTTCCTAGATTCACCAGT
GATCCCTATCTGCCTTTGGTGACATGGAAGACAGGGTAAGACAAGAAGTTTTCTGGCTATACTAGGACCTTCTCAGCCAT
AAATCTTTATTCAGGACTCAGGGAATATATGTTAACCAGTGCACTTAAGGACAGTTGATCTCCCCCTTGACCTGAGAGGA
GCTGCCTAAACTTTTCTGCTCTATCTCCTTACTAACTTCG

Alignment

ORF - retro_ecab_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 64.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKRRCVPPLEPKLAAGCCGVKKPKLSGSGTHSHGNQSTTVPGSSSGPLQNHQHVDGSSGRENVSDLTLG
          MGKR..V.PL.PKLA..CCGVKK.KL.G.GTHSH.NQSTTVPGSSSG..QNH.HV.GSSG.ENV.DLTLG
Retrocopy MGKRHRVSPLKPKLAECCCGVKKLKLPGNGTHSHRNQSTTVPGSSSGHFQNHKHVGGSSGQENVLDLTLG

Parental  PGNSP-ITRMNPASGALSPLPRPNGTANTAKNLVVTAEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLF
          ..NSP.I..MNP.SGALSPL..PNGT.N..KNLVVTAEMCCYCFD..YCHLYGFPQ..LPRFT.DPY...
Retrocopy SRNSP>IIQMNPSSGALSPLLGPNGTTNNTKNLVVTAEMCCYCFDIFYCHLYGFPQSQLPRFTSDPYLPL

Parental  VTWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFP-PLTREELPKLFCSVSLLTN
          VTWKTG.DK...G...TFSA.NL.SGLREY.LTSALKDS..P.PLT.EELPKLFCS.SLLT.
Retrocopy VTWKTG*DKKFSGYTRTFSAINLYSGLREYMLTSALKDS*SP<PLT*EELPKLFCSISLLTS

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	9.62 RPM
SRP021940_cerebellum	0.00 RPM	11.84 RPM
SRP021940_embryo	0.00 RPM	18.92 RPM
SRP021940_placental_villous	0.00 RPM	22.23 RPM
SRP021940_synovial_membrane	0.00 RPM	18.59 RPM
SRP021940_testis	0.00 RPM	29.93 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1085 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085 ,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,