RetrogeneDB ID: retro_ecab_215

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:36267306..36267715(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX6
• Ensembl ID: ENSECAG00000022468
• Aliases: None
• Description: peroxiredoxin 6 [Source:HGNC Symbol;Acc:16753]

Sequence

>retro_ecab_215
CAGGATATCAATGTTTACAGTGGTAAGAAGCCCACAGAAATGTTACTTTTTCCCATCATTGATGAAAAGGATTAGGACCT
GGCCATTGTGTAGGTATGATGAATCCAGTAGAGAAAAGGAACAGGGCATGCCTGTGACAGCATGTGTGGTGTTTATTTTT
GGTCCTAATAAGAAACTGAAGTTATCTATCCTCTACACAGCCGCCACTGGCAGATGCTTTGATGAGATTCTTGGAGTAGC
TATTTCTCTCCAGCTGACAGCCAAAAAGTGGTTTGACACCCTGGTTGATTGGAAGAATGGAGATAGCATGGTGGTCCTTC
CAATCATCCCTTCCAAACTTTCCCCTAAAGGAGTCGTCACCAAAGAGCTCCTATCTGGCAAGAAATACCTCTGCTACCCT
CCCAAGCCT

Alignment

ORF - retro_ecab_215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.13 %
• Parental protein coverage: 62.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDINAYNGDEPKETLPFPIIDDKNRDLAIL-LGMLDPAEK-DEKGMPVTARVVFIFGPDKKLKLSILYPA
          .DIN.Y.G..P.E.L.FPIID.K..DLAI...GM..P.EK..E.GMPVTA.VVFIFGP.KKLKLSILY.A
Retrocopy QDINVYSGKKPTEMLLFPIIDEKD*DLAIV<VGMMNPVEK<KEQGMPVTACVVFIFGPNKKLKLSILYTA

Parental  TTGRNFDEILRVVISLQLTAEKRVATPVDWKDGDSVMVLPTIPEEEAKKLFPKGVFTKELPSGKKYLRYT
          .TGR.FDEIL.V.ISLQLTA.K...T.VDWK.GDS..VLP.IP.....KL.PKGV.TKEL.SGKKYL.Y.
Retrocopy ATGRCFDEILGVAISLQLTAKKWFDTLVDWKNGDSMVVLPIIP----SKLSPKGVVTKELLSGKKYLCYP

Parental  PQP
          P.P
Retrocopy PKP

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	125.73 RPM
SRP021940_cerebellum	0.00 RPM	62.11 RPM
SRP021940_embryo	0.00 RPM	123.11 RPM
SRP021940_placental_villous	0.00 RPM	50.37 RPM
SRP021940_synovial_membrane	0.00 RPM	74.12 RPM
SRP021940_testis	0.00 RPM	286.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_215 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_215 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_492

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015560	1 retrocopy	retro_amel_493,
Bos taurus	ENSBTAG00000004855	2 retrocopies	retro_btau_1325, retro_btau_1477,
Canis familiaris	ENSCAFG00000014579	1 retrocopy	retro_cfam_492,
Choloepus hoffmanni	ENSCHOG00000011367	6 retrocopies	retro_chof_1143, retro_chof_1361, retro_chof_1364, retro_chof_225, retro_chof_2483, retro_chof_2598,
Callithrix jacchus	ENSCJAG00000009355	6 retrocopies	retro_cjac_1903, retro_cjac_2188, retro_cjac_3008, retro_cjac_3239, retro_cjac_3830, retro_cjac_4000,
Cavia porcellus	ENSCPOG00000011091	1 retrocopy	retro_cpor_623,
Equus caballus	ENSECAG00000022468	1 retrocopy	retro_ecab_215 ,
Erinaceus europaeus	ENSEEUG00000004040	1 retrocopy	retro_eeur_475,
Homo sapiens	ENSG00000117592	2 retrocopies	retro_hsap_1046, retro_hsap_3017,
Gorilla gorilla	ENSGGOG00000026357	1 retrocopy	retro_ggor_2086,
Macaca mulatta	ENSMMUG00000008776	1 retrocopy	retro_mmul_1928,
Monodelphis domestica	ENSMODG00000004032	2 retrocopies	retro_mdom_462, retro_mdom_661,
Mustela putorius furo	ENSMPUG00000004648	1 retrocopy	retro_mputfur_1328,
Mus musculus	ENSMUSG00000026701	2 retrocopies	retro_mmus_181, retro_mmus_2334,
Nomascus leucogenys	ENSNLEG00000015278	2 retrocopies	retro_nleu_2244, retro_nleu_917,
Pan troglodytes	ENSPTRG00000042455	1 retrocopy	retro_ptro_70,
Pteropus vampyrus	ENSPVAG00000002596	2 retrocopies	retro_pvam_1389, retro_pvam_805,
Rattus norvegicus	ENSRNOG00000002896	3 retrocopies	retro_rnor_2084, retro_rnor_754, retro_rnor_806,
Sarcophilus harrisii	ENSSHAG00000003248	1 retrocopy	retro_shar_478,
Tarsius syrichta	ENSTSYG00000010073	2 retrocopies	retro_tsyr_1395, retro_tsyr_193,
Tursiops truncatus	ENSTTRG00000008478	1 retrocopy	retro_ttru_1274,