RetrogeneDB ID: retro_ecab_472

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:19699165..19699743(-)
• Located in intron of: ENSECAG00000007560

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT4
• Ensembl ID: ENSECAG00000019319
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 4 [Source:HGNC Symbol;Acc:8051]

Sequence

>retro_ecab_472
CGGCGGCAGCCGGAGCAGCAGCGGCAGCAAGGGCCCGCCTCTATGATGAAGTTCAAGCCCAACCAGACGCGGACCTACGA
CCACGAGGGCTTCAAGAAGCGGGCAGTGTGCCTGTGCTTCCGGAGCGAGCAAGAGGACGAGGTGCTGTTGGTGAGAAGCA
GTCCGTACCCAGACCAATGGATTGTCCCAGGAGGAGGCGGGGAGCCCGATGAGGAGCCTGGCGGTGCTGCGGTGAGGGAG
GTTTATGAAGACGCTGGGTCAAAGGAAAATTAGGCAGACTCCTGGGCATATTTGAGAACCAAGACCGAAAGCACAGGACA
TATGTTTATGTTCTTACTGTCACTGAAATATTAGAAGATTGGGAAGATTCTGTTAATAGAGGAAGGAAGAGAGAGTGGTT
CAAAGTTGAAGATGCTATCAAAGTTCTCCAGTGTCATAAGCCTGTACATGCAGAGTATCTGGAAAAACTAAAGCTGAGGT
GTTCTCCATCCAATGACAATTCCACTGTCCCTTCCCCTCCAGATAATAACACCTTGTTTGTAACTGCTGCACAGACCCCT
GGGTTGCCATCTAGTATA

Alignment

ORF - retro_ecab_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.72 %
• Parental protein coverage: 91.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRRMEQQRHQEPASMMKFKPNQTRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMEPE
          RR..EQQR.Q.PASMMKFKPNQTRTYD.EGFKKRA.CLCFRSEQEDEVLLV.SS.YPDQWIVPGGG.EP.
Retrocopy RRQPEQQRQQGPASMMKFKPNQTRTYDHEGFKKRAVCLCFRSEQEDEVLLVRSSPYPDQWIVPGGGGEPD

Parental  EEPGGAAVREVYEEAG-VKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDA
          EEPGGAAVREVYE.AG.VKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDWEDSVN.GRKREWFKVEDA
Retrocopy EEPGGAAVREVYEDAG<VKGKLGRLLGIFENQDRKHRTYVYVLTVTEILEDWEDSVNRGRKREWFKVEDA

Parental  IRVLQCHKPVHAEYLQKLKLGCSPSNGNSTVPSLPDNNTLFVTAAQTPGLPSSI
          I.VLQCHKPVHAEYL.KLKL.CSPSN.NSTVPS.PDNNTLFVTAAQTPGLPSSI
Retrocopy IKVLQCHKPVHAEYLEKLKLRCSPSNDNSTVPSPPDNNTLFVTAAQTPGLPSSI

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	13.93 RPM
SRP021940_cerebellum	0.00 RPM	13.45 RPM
SRP021940_embryo	0.18 RPM	33.17 RPM
SRP021940_placental_villous	0.00 RPM	37.67 RPM
SRP021940_synovial_membrane	0.14 RPM	40.41 RPM
SRP021940_testis	0.06 RPM	29.16 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_472 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_472 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009844	2 retrocopies	retro_amel_1401, retro_amel_36,
Dasypus novemcinctus	ENSDNOG00000015207	3 retrocopies	retro_dnov_1906, retro_dnov_2555, retro_dnov_41,
Dipodomys ordii	ENSDORG00000000647	3 retrocopies	retro_dord_26, retro_dord_272, retro_dord_660,
Equus caballus	ENSECAG00000019319	1 retrocopy	retro_ecab_472 ,
Echinops telfairi	ENSETEG00000013922	2 retrocopies	retro_etel_1627, retro_etel_2111,
	ENSG00000173598	0 retrocopies
Gorilla gorilla	ENSGGOG00000014324	1 retrocopy	retro_ggor_108,
Loxodonta africana	ENSLAFG00000013776	1 retrocopy	retro_lafr_1131,
Microcebus murinus	ENSMICG00000007100	2 retrocopies	retro_mmur_1521, retro_mmur_1565,
Myotis lucifugus	ENSMLUG00000002767	1 retrocopy	retro_mluc_753,
Monodelphis domestica	ENSMODG00000009468	1 retrocopy	retro_mdom_214,
Mus musculus	ENSMUSG00000020029	3 retrocopies	retro_mmus_1201, retro_mmus_1202, retro_mmus_1203,
Oryctolagus cuniculus	ENSOCUG00000011283	1 retrocopy	retro_ocun_1905,
Pteropus vampyrus	ENSPVAG00000013730	1 retrocopy	retro_pvam_1423,
Ictidomys tridecemlineatus	ENSSTOG00000020306	1 retrocopy	retro_itri_112,
Tupaia belangeri	ENSTBEG00000012198	7 retrocopies	retro_tbel_1705, retro_tbel_2322, retro_tbel_3443, retro_tbel_3472, retro_tbel_3733, retro_tbel_3739, retro_tbel_4678,
Tursiops truncatus	ENSTTRG00000003309	2 retrocopies	retro_ttru_1625, retro_ttru_1925,
Vicugna pacos	ENSVPAG00000002957	1 retrocopy	retro_vpac_507,