RetrogeneDB ID: retro_ecab_1016

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:67400866..67401376(+)
• Located in intron of: ENSECAG00000026944

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM1
• Ensembl ID: ENSECAG00000021950
• Aliases: None
• Description: nucleophosmin (nucleolar phosphoprotein B23, numatrin) [Source:HGNC Symbol;Acc:7910]

Sequence

>retro_ecab_1016
GACATGGACATGAGCCCCCTGAGGCCCCAGAACTATCTTTTGAGTTGTGAACTAAATGCTGACAAAGATTATCACTCTAA
GGTGGAAAATGCTGAAAATGAACACTAGTTATCTTTAAGAATGGTCAGTTTAGGGGCTGATGCAAAGGATGAATTGCACA
TTGTTGAAGCAGAGGCAATGACTTATGAAGGCAGTCCAATTAAAGTAATACTGGCAACTTTGAAAATGTCTGTACAGCCA
ACAGTTTCCCTTGGGGGCTTTGAAATAACACCACCTGTGATCTTACAATTGAAGTGTGGTTCAGGGCCTGTGCAAATTAG
TGGATGGCACTTAGTAGCTGTGGAAGAAGATGCAGAATCAGGTGATGAAGAGGAGAAGGATGTGAAACTCTTTAGTATAT
CTGGAATGCCTTCTGCCCCTGGAAGTGGTAGCAAGGTTCGACAGAAAAAAGTAAAAACTTGCCCAGATGAAGATGATGAT
GATGATTTTGATGAGGCGGAAGCTGAAGAA

Alignment

ORF - retro_ecab_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVT
          DMDMSPLRPQNYL..CEL.ADKDYH.KV.N.ENEH.LSLR.VSLGA.AKDELHIVEAEAM.YEGSPIKV.
Retrocopy DMDMSPLRPQNYLLSCELNADKDYHSKVENAENEH*LSLRMVSLGADAKDELHIVEAEAMTYEGSPIKVI

Parental  LATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGKRSAP
          LATLKMSVQPTVSLGGFEITPPV.L.LKCGSGPV.ISG.HLVAVEEDAES.DEEE.DVKL.SISG..SAP
Retrocopy LATLKMSVQPTVSLGGFEITPPVILQLKCGSGPVQISGWHLVAVEEDAESGDEEEKDVKLFSISGMPSAP

Parental  GSGSKVPQKKVKLAADEDDDDEDDDEDDDE
          GSGSKV.QKKVK...DEDDDD..D.....E
Retrocopy GSGSKVRQKKVKTCPDEDDDDDFDEAEAEE

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	112.98 RPM
SRP021940_cerebellum	0.05 RPM	51.78 RPM
SRP021940_embryo	0.33 RPM	208.67 RPM
SRP021940_placental_villous	0.00 RPM	73.32 RPM
SRP021940_synovial_membrane	0.11 RPM	57.62 RPM
SRP021940_testis	0.00 RPM	45.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1016 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003910	1 retrocopy	retro_amel_983,
Bos taurus	ENSBTAG00000015316	2 retrocopies	retro_btau_538, retro_btau_56,
Canis familiaris	ENSCAFG00000016912	3 retrocopies	retro_cfam_22, retro_cfam_286, retro_cfam_900,
Callithrix jacchus	ENSCJAG00000019334	13 retrocopies	retro_cjac_1559, retro_cjac_1682, retro_cjac_1696, retro_cjac_1733, retro_cjac_2075, retro_cjac_2351, retro_cjac_2368, retro_cjac_2533, retro_cjac_2605, retro_cjac_3270, retro_cjac_3416, retro_cjac_4117, retro_cjac_838,
Equus caballus	ENSECAG00000021950	4 retrocopies	retro_ecab_1016 , retro_ecab_1100, retro_ecab_393, retro_ecab_544,
Felis catus	ENSFCAG00000030268	3 retrocopies	retro_fcat_156, retro_fcat_376, retro_fcat_720,
Gorilla gorilla	ENSGGOG00000007220	12 retrocopies	retro_ggor_1543, retro_ggor_1660, retro_ggor_1976, retro_ggor_2453, retro_ggor_2454, retro_ggor_2539, retro_ggor_2559, retro_ggor_2571, retro_ggor_2681, retro_ggor_2959, retro_ggor_560, retro_ggor_591,
Macaca mulatta	ENSMMUG00000015781	1 retrocopy	retro_mmul_203,
Mus musculus	ENSMUSG00000057113	5 retrocopies	retro_mmus_1301, retro_mmus_1798, retro_mmus_3131, retro_mmus_539, retro_mmus_550,
Otolemur garnettii	ENSOGAG00000013616	14 retrocopies	retro_ogar_1554, retro_ogar_1623, retro_ogar_1671, retro_ogar_1776, retro_ogar_2015, retro_ogar_2168, retro_ogar_2207, retro_ogar_2461, retro_ogar_2605, retro_ogar_2832, retro_ogar_3037, retro_ogar_536, retro_ogar_595, retro_ogar_614,
Pongo abelii	ENSPPYG00000016037	7 retrocopies	retro_pabe_2405, retro_pabe_3072, retro_pabe_3261, retro_pabe_3627, retro_pabe_3699, retro_pabe_486, retro_pabe_532,