RetrogeneDB ID: retro_ecab_827

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:36467356..36467769(+)
• Located in intron of: ENSECAG00000022307

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012620
• Aliases: None
• Description: None

Sequence

>retro_ecab_827
GAGCTGATGGAGCGAGTAAAATCTGAGCTTGAGCAGCTGAGAGAGAAATGCAACACGGTGCAGGTATGAGTGCAGCTGCT
CATCCCGAAGGTGGAGGACGACAAGAACTTCAGAGTGGCTATCCAGGAAGACACCGTGGACCAGCTGTGGACCATGAAGA
GCACAGCTGCCTCCTGTCTACGCCACTTCTCCACCTACTGCAACACCCAGGCCAAGATGGTATCCAAAATAGTGAAATAC
TCGCAGATGGAAGATGATCTCTGCACTGTAGCCAAGGTTGATGAAAAGGAGTACTTTAGTGTACGCCAGATCTTACTGCA
TGTGCGGAGCCAGTATCCACCTTGCGTGATGTAATCCTCAGAACCATTGAGAAGAGCAAGACTCCTTGGAGCACCAACAC
TGACAAGTAGTAC

Alignment

ORF - retro_ecab_827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.52 %
• Parental protein coverage: 54.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLDQISRYYITR
          ...E.VK.E...L.EKCNTV...VQLLIP..ED..NF.V.IQE.TV..L.T..S.AAS.L...S.Y..T.
Retrocopy ELMERVKSELEQLREKCNTVQV*VQLLIPKVEDDKNFRVAIQEDTVDQLWTMKSTAASCLRHFSTYCNTQ

Parental  AKLVSKIAKYPHVEDYRRTVTEIDEKEYISLRLIISELRNQY-VTLHDMILKNIEKIKRPRSSNAETLY
          AK.VSKI.KY...ED...TV...DEKEY.S.R.I....R.QY..TL.D.IL..IEK.K.P.S.N....Y
Retrocopy AKMVSKIVKYSQMEDDLCTVAKVDEKEYFSVRQILLHVRSQY<STLRDVILRTIEKSKTPWSTNTDK*Y

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	5.08 RPM
SRP021940_cerebellum	0.00 RPM	9.40 RPM
SRP021940_embryo	0.00 RPM	9.72 RPM
SRP021940_placental_villous	0.00 RPM	6.78 RPM
SRP021940_synovial_membrane	0.00 RPM	5.76 RPM
SRP021940_testis	0.00 RPM	26.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_827 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_827 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_245
Pan troglodytes	retro_ptro_212
Pongo abelii	retro_pabe_413
Oryctolagus cuniculus	retro_ocun_641
Bos taurus	retro_btau_1249
Sus scrofa	retro_sscr_784

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013688	2 retrocopies	retro_acar_118, retro_acar_37,
Bos taurus	ENSBTAG00000019918	2 retrocopies	retro_btau_1249, retro_btau_941,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307,
Cavia porcellus	ENSCPOG00000012552	1 retrocopy	retro_cpor_1204,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827 ,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Loxodonta africana	ENSLAFG00000013446	1 retrocopy	retro_lafr_725,
Mustela putorius furo	ENSMPUG00000010027	1 retrocopy	retro_mputfur_619,
Oryctolagus cuniculus	ENSOCUG00000015986	1 retrocopy	retro_ocun_641,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,