RetrogeneDB ID: retro_ecab_239

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:41594730..41594996(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSECAG00000016939
• Aliases: None
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_ecab_239
AGGAAATTCATGACCAATGAGTGCTTTGATAGGAAGAGTAGATCAAAGATATCCTTTACCCTGGAAAAGCAACATTATTC
ATGACTGAAATACTAGCCAAATTGTCCAAGACTATACTGGATATTATTTTGGACTTCCGATTCAGAACTCTTTTTGATAA
GACAACAGAATTTGATATGGTTTATGTTCTTTTAATTAGGATAAAATAAAATCCCCAACAGAGACTTGCAAAGCATGGCC
TAAGTAAGAAGAAAAATATTTTGAGA

Alignment

ORF - retro_ecab_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.04 %
• Parental protein coverage: 72.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKFMTNRLLQRKQM-VIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTTGFGMIYDS
          RKFMTN....RK.....D.L.PGKAT...TEI...LAK..KT..D.I..F.FRT.F...KTT.F.M.Y..
Retrocopy RKFMTNECFDRKSR<IKDILYPGKATLFMTEI---LAKLSKTILDIILDFRFRTLF--DKTTEFDMVYVL

Parental  LDYAKKNEPKHRLARHGLYEKKKTSR
          L...K.N.P..RLA.HGL..KK...R
Retrocopy LIRIK*N-PQQRLAKHGLSKKKNILR

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	0.06 RPM	363.39 RPM
SRP021940_cerebellum	0.00 RPM	178.44 RPM
SRP021940_embryo	0.03 RPM	346.31 RPM
SRP021940_placental_villous	0.05 RPM	206.78 RPM
SRP021940_synovial_membrane	0.00 RPM	221.32 RPM
SRP021940_testis	0.00 RPM	165.93 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_239 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_239 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016939	5 retrocopies	retro_ecab_239 , retro_ecab_398, retro_ecab_422, retro_ecab_514, retro_ecab_746,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Microcebus murinus	ENSMICG00000005951	7 retrocopies	retro_mmur_1308, retro_mmur_132, retro_mmur_1338, retro_mmur_1636, retro_mmur_217, retro_mmur_583, retro_mmur_902,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706, retro_mdom_1914,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,