RetrogeneDB ID: retro_ecab_460

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:22019873..22020449(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDRBS3
• Ensembl ID: ENSECAG00000010194
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 3 [Source:HGNC Symbol;Acc:18117]

Sequence

>retro_ecab_460
TTCCTCATTCCTGACTATAATGATGACCTCAGGCAAGCACACCTCCAGGAATTAACATATTTGAATGGTGGCTCAGAAAA
TGCAGATGTACCCATTGTTTGAGGGAAATCCACCTTGCATACAAGAGGTATCCTAACCCCAGCAATAACCAGGGGAAGGG
GAGGAGTCACGGCCCAGCAGGGTGGAGTTGGTGTGCCACAAGGGATGCCAACTTCCAGGGGAGTCCTTTCCACCAGAGGG
CCAGTGCATCAGGGAAGAGGACTGCTCACTCCCAGAGCAAGAGGAGTGCCCCCAACTGGGCAGACCTCCACAGCCAGCCC
CAACACAAGAGACCTATGGAGATTATGACTATGATGTGGATATGACACTGCTTATGATGAACAGAGTTATGATTCCTATG
ATGACAGCTATAGCACCCCAGCCCAAAGTGGTGCTGATGACTATGATTATGGACATGGAGTCAGTGAAGAGACTTATGAT
TCCCATGGGCAAGAGGAGTGGCCTAACTCAAGACACAAGGCACCTTCAGCGAGGACAGCAAAGGGCATCTACAGAGACCA
TCCCTATGGCAGATAC

Alignment

ORF - retro_ecab_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.59 %
• Parental protein coverage: 55.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKSTLRTRGVPTPAITRGRGGVTARPVGVGVPRGTP
          FLIPDYND..RQA.LQELTYLNGGSENADVP.V.GKSTL.TRG..TPAITRGRGGVTA...GVGVP.G.P
Retrocopy FLIPDYNDDLRQAHLQELTYLNGGSENADVPIV*GKSTLHTRGILTPAITRGRGGVTAQQGGVGVPQGMP

Parental  TSRGVLSTRGPVSRGRGLLTPRARGVPPTGYR-PPPPPPTQETYGDYDYD-DGYGTAYDEQSYDSYDNSY
          TSRGVLSTRGPV..GRGLLTPRARGVPPTG...P.P..PTQETYGDYDYD..GY.TAYDEQSYDSYD.SY
Retrocopy TSRGVLSTRGPVHQGRGLLTPRARGVPPTGQT>PQP-APTQETYGDYDYD<CGYDTAYDEQSYDSYDDSY

Parental  STPVQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARTAKGVYRDQPYGRY
          STP.QSGAD.YDYGHG.SEETYDS.GQEEW.NSRHKAPSARTAKG.YRD.PYGRY
Retrocopy STPAQSGADDYDYGHGVSEETYDSHGQEEWPNSRHKAPSARTAKGIYRDHPYGRY

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	0.00 RPM
SRP021940_cerebellum	0.26 RPM	5.92 RPM
SRP021940_embryo	0.56 RPM	34.52 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.08 RPM	1.65 RPM
SRP021940_testis	0.00 RPM	67.27 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_460 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_460 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085, retro_dnov_1131,
Dipodomys ordii	ENSDORG00000014595	1 retrocopy	retro_dord_689,
Equus caballus	ENSECAG00000010194	1 retrocopy	retro_ecab_460 ,
Otolemur garnettii	ENSOGAG00000005150	3 retrocopies	retro_ogar_2456, retro_ogar_3114, retro_ogar_550,
Sarcophilus harrisii	ENSSHAG00000000632	1 retrocopy	retro_shar_179,
Tursiops truncatus	ENSTTRG00000001270	2 retrocopies	retro_ttru_1633, retro_ttru_1929,