RetrogeneDB ID: retro_ecab_1054

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:19373324..19374075(+)
• Located in intron of: ENSECAG00000008328

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000017673
• Aliases: None
• Description: None

Sequence

>retro_ecab_1054
GAGGTTGGCCACTTAATCCAGGTTGCTGCGGGGAGAAGTAATCTCAAGAGAGTGACCCTGGAACTGGGGAGAAAGAACCC
CAACATTATCATGTCAGATGCTGATGTGGACTGGGCCTGGAGCCCACTTTGCCCTGTTCTTCAACCAGGGCCAGTGCTAC
TGTGTGGGCTCGCAGACCTTTGTGCAGGAGGGTGTTTATGCCATGTGCATGGAGCTGGGCATCACCCCTGCCAGTTCTCA
TGTAGTTGGGAACTCCTTTGACAGCTAGACCAAGCAAGGGCCACAGATGGATGAAACTCAGTTTAAGAACGTCCTTGACT
GTACTGAATCTTGGAAAGAGGAGGGGACAAAGCTGCTGTGTGGTGGAGGGGCGGCTGCTGACCGTGGCTACTTCATCCAG
CCCACTGTGTTAGGAGATGTGCAAGATGACATGACCATCACAAAGGAGATCTTTGGGCTAGTGATGCAGATCCTGAAGTT
CAAGACCATAAAAGAAGTTGTTGAGAGAGCCAACAATTCCAAGCACAGGCTGGCTGCAGCTGTCTTCACAAAAGACTTGG
ACAAGGCCAATTCTCTGTCCCAAGCCCTCCAGGCTGGCACTTTGTGGGTCAACTGCTATGATGTATCTGGGGCCCGGCCA
CCGTTTGGTGGCTACAAGATGTCTGGGAATGGTGGGGACCCGGGAGAGTATGGTCTGCAGGCATATACTGAAATGAAAAC
CGTTACAGTCAAAGTTCCTCAGAAGAACTCA

Alignment

ORF - retro_ecab_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVGHLIQVAAGRSNLKKVTLELGGKSPNIIMSDADMD-WAVEQAHFALFFNQGQCCCAGSRTFVQEDVYA
          EVGHLIQVAAGRSNLK.VTLELG.K.PNIIMS..D.D.W....AHFALFFNQGQC.C.GS.TFVQE.VYA
Retrocopy EVGHLIQVAAGRSNLKRVTLELGRKNPNIIMS--DAD>WTGPGAHFALFFNQGQCYCVGSQTFVQEGVYA

Parental  EFVERSVARARSRVVGNPFDSQTEQGPQVDETQFNKVLGYIKSGKEEGAKLLCGGGAAADRGYFIQPTVF
          ...E.....A.S.VVGN.FDS.T.QGPQ.DETQF..VL....S.KEEG.KLLCGGGAAADRGYFIQPTV.
Retrocopy MCMELGITPASSHVVGNSFDS*TKQGPQMDETQFKNVLDCTESWKEEGTKLLCGGGAAADRGYFIQPTVL

Parental  GDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWINCY
          GDVQD.MTI.KE.IFG.VMQILKFKTI.EVV.RANNSK..LAAAVFTKDLDKAN.LSQALQAGT.W.NCY
Retrocopy GDVQDDMTITKE-IFGLVMQILKFKTIKEVVERANNSKHRLAAAVFTKDLDKANSLSQALQAGTLWVNCY

Parental  DVFGAQSPFGGYKMSGNGRELGEYGLQAYTEVKTVTIKVPQKNS
          DV.GA..PFGGYKMSGNG...GEYGLQAYTE.KTVT.KVPQKNS
Retrocopy DVSGARPPFGGYKMSGNGGDPGEYGLQAYTEMKTVTVKVPQKNS

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	300.46 RPM
SRP021940_cerebellum	0.00 RPM	217.39 RPM
SRP021940_embryo	0.03 RPM	125.79 RPM
SRP021940_placental_villous	0.00 RPM	129.52 RPM
SRP021940_synovial_membrane	0.03 RPM	191.67 RPM
SRP021940_testis	0.06 RPM	302.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1054 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1054 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013664	1 retrocopy	retro_amel_51,
Bos taurus	ENSBTAG00000008743	1 retrocopy	retro_btau_48,
Canis familiaris	ENSCAFG00000008683	1 retrocopy	retro_cfam_1493,
Equus caballus	ENSECAG00000017673	2 retrocopies	retro_ecab_1054 , retro_ecab_1061,
Felis catus	ENSFCAG00000022000	1 retrocopy	retro_fcat_1590,
Homo sapiens	ENSG00000111275	1 retrocopy	retro_hsap_19,
Gorilla gorilla	ENSGGOG00000007108	1 retrocopy	retro_ggor_33,
Latimeria chalumnae	ENSLACG00000011798	1 retrocopy	retro_lcha_108,
Microcebus murinus	ENSMICG00000003487	1 retrocopy	retro_mmur_19,
Myotis lucifugus	ENSMLUG00000017084	1 retrocopy	retro_mluc_1918,
Macaca mulatta	ENSMMUG00000008336	1 retrocopy	retro_mmul_247,
Mustela putorius furo	ENSMPUG00000002282	1 retrocopy	retro_mputfur_27,
Mus musculus	ENSMUSG00000029455	1 retrocopy	retro_mmus_222,
Nomascus leucogenys	ENSNLEG00000000016	1 retrocopy	retro_nleu_22,
Otolemur garnettii	ENSOGAG00000033093	1 retrocopy	retro_ogar_203,
Pongo abelii	ENSPPYG00000004966	1 retrocopy	retro_pabe_32,
Pteropus vampyrus	ENSPVAG00000013189	1 retrocopy	retro_pvam_163,
Rattus norvegicus	ENSRNOG00000001344	1 retrocopy	retro_rnor_307,
Sus scrofa	ENSSSCG00000009889	1 retrocopy	retro_sscr_9,
Ictidomys tridecemlineatus	ENSSTOG00000015009	1 retrocopy	retro_itri_33,
Xenopus tropicalis	ENSXETG00000020930	1 retrocopy	retro_xtro_12,