RetrogeneDB ID: retro_ecab_184

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:115917239..115917665(-)
• Located in intron of: ENSECAG00000005595

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCRB1
• Ensembl ID: ENSECAG00000012174
• Aliases: None
• Description: zinc finger CCHC-type and RNA binding motif 1 [Source:HGNC Symbol;Acc:29620]

Sequence

>retro_ecab_184
ATCATAAAGTTTACTGTTAGAAAAAAAGATGCTGAGAAGAGTAAAGGGGTTGGGTTTATTTATTTATTTTTTTGGATAGG
AATCTGAATAAAACTATACCAGCCATTAAACAGCAGTTACTTGGTTGTGTAATAAAAGCAAGCATTGCTACTGACAACTG
AAGAGCAGCTGAATTCATCTGAAGGTAAAACTGCTTTGATAAATCTAATGAATGTAGGGAAGCGGACCCTTGTGTTATAC
CTGTCTTGAAAATATGCATAGAGAATGTGAACTACCACAAAAGAAAGAGAAAAAGAAAAAAGAGAAAATCTCAGATCCTG
AAGAAGAAAGTGAGGAAGTAGAAGAAAGTGAAGATGAAGGGGAAAACCCTGCATTTGGCACCTCAGCCAGGTTGTAGCTT
TCCAGCAAACCAACACTGAAAAAGAT

Alignment

ORF - retro_ecab_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.68 %
• Parental protein coverage: 67.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVKVTIMKDKDTRRSKGVAFI-LFLDKDSAQNCTRAINNKQLFGRVIKASIAIDNGRAAEFIRRRNYFDK
          ..K.T..K.KD...SKGV.FI.LF...D...N.T......QL.G.VIKASIA.DN.RAAEFI.R.N.FDK
Retrocopy IIKFTVRK-KDAEKSKGVGFI<LFIFLDRNLNKTIPAIKQQLLGCVIKASIATDN*RAAEFI*R*NCFDK

Parental  SKCYECGE-SGHLSYACPKNMLGEREPPKKKEKKKKKKIPEPEEEIEGVEESEDEGEDPALDS-LSQAIA
          S...EC.E.SG.L.Y.C..NM..E.E.P.............PEEE.E.VEESEDEGE.PA....LSQ..A
Retrocopy SN--ECRE<SGPLCYTCLENMHRECELPXXXXXXXXXXXSDPEEESEEVEESEDEGENPAFGT<LSQVVA

Parental  FQQAKIEEE
          FQQ...E..
Retrocopy FQQTNTEKD

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	0.05 RPM	0.00 RPM
SRP021940_embryo	0.10 RPM	9.23 RPM
SRP021940_placental_villous	0.00 RPM	5.68 RPM
SRP021940_synovial_membrane	0.00 RPM	7.47 RPM
SRP021940_testis	0.13 RPM	27.43 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_184 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019119	2 retrocopies	retro_btau_1637, retro_btau_830,
Choloepus hoffmanni	ENSCHOG00000004490	1 retrocopy	retro_chof_1549,
Callithrix jacchus	ENSCJAG00000017749	3 retrocopies	retro_cjac_2009, retro_cjac_2662, retro_cjac_4174,
Cavia porcellus	ENSCPOG00000014554	1 retrocopy	retro_cpor_757,
Dasypus novemcinctus	ENSDNOG00000010107	11 retrocopies	retro_dnov_1075, retro_dnov_1120, retro_dnov_1127, retro_dnov_1357, retro_dnov_1599, retro_dnov_1673, retro_dnov_1846, retro_dnov_2146, retro_dnov_2432, retro_dnov_2466, retro_dnov_888,
Equus caballus	ENSECAG00000012174	1 retrocopy	retro_ecab_184 ,
Erinaceus europaeus	ENSEEUG00000000397	1 retrocopy	retro_eeur_298,
Echinops telfairi	ENSETEG00000019302	1 retrocopy	retro_etel_2080,
Gorilla gorilla	ENSGGOG00000015647	1 retrocopy	retro_ggor_3029,
Loxodonta africana	ENSLAFG00000008847	2 retrocopies	retro_lafr_1183, retro_lafr_783,
Microcebus murinus	ENSMICG00000017422	3 retrocopies	retro_mmur_1236, retro_mmur_236, retro_mmur_466,
Myotis lucifugus	ENSMLUG00000001332	3 retrocopies	retro_mluc_2290, retro_mluc_319, retro_mluc_364,
Monodelphis domestica	ENSMODG00000008893	1 retrocopy	retro_mdom_114,
Mus musculus	ENSMUSG00000022635	1 retrocopy	retro_mmus_847,
Oryctolagus cuniculus	ENSOCUG00000013664	2 retrocopies	retro_ocun_742, retro_ocun_896,
Otolemur garnettii	ENSOGAG00000013178	2 retrocopies	retro_ogar_43, retro_ogar_812,
Ochotona princeps	ENSOPRG00000011095	2 retrocopies	retro_opri_729, retro_opri_927,
Procavia capensis	ENSPCAG00000011749	2 retrocopies	retro_pcap_458, retro_pcap_64,
Pan troglodytes	ENSPTRG00000004838	1 retrocopy	retro_ptro_3231,
Pteropus vampyrus	ENSPVAG00000006651	2 retrocopies	retro_pvam_1343, retro_pvam_697,