RetrogeneDB ID: retro_ecab_634

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:12154095..12154361(-)
• Located in intron of: ENSECAG00000014561

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000006469
• Aliases: None
• Description: None

Sequence

>retro_ecab_634
GAGGATGAATAAGAGCATGCTCAGGTAACCAAATGTTGGAAAATGGATGATTAGAAGCAATGAGTTTTGATGGTGTAAAG
TGGTTATGTCCTATCAAAGGAAAACTTAGAAAAACGGTTTGAATAAATACCTCAGACGGTATTTTGGTTGGTCTGCCAGA
CTATGGAGATAACAAAGCTGAGGTAATTTTAAAATACAATGCAGATGAAGGTATAAGTCTTAAGGCATATGGCAAGCTTC
CAAAATATGCTAAAATCAATGAAACA

Alignment

ORF - retro_ecab_634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 61.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDGQEYAQVIK-MLGNGRLEAMCFDGIKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNAD
          ED..E.AQV.K.ML.NG.LEAM.FDG.K.LC.I.GKLRK.V.INTSD.ILVGL.DY.DNKA.VILKYNAD
Retrocopy EDE*EHAQVTK<MLENG*LEAMSFDGVKWLCPIKGKLRKTV*INTSDGILVGLPDYGDNKAEVILKYNAD

Parental  EARSLKAYGELPEHAKINET
          E..SLKAYG.LP..AKINET
Retrocopy EGISLKAYGKLPKYAKINET

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	15.41 RPM
SRP021940_cerebellum	0.00 RPM	17.35 RPM
SRP021940_embryo	0.00 RPM	18.92 RPM
SRP021940_placental_villous	0.00 RPM	21.70 RPM
SRP021940_synovial_membrane	0.00 RPM	11.39 RPM
SRP021940_testis	0.00 RPM	11.13 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_634 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_634 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_634 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1431
Pan troglodytes	retro_ptro_978
Gorilla gorilla	retro_ggor_1103
Pongo abelii	retro_pabe_1185
Sus scrofa	retro_sscr_948

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464, retro_ecab_634 ,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839,