RetrogeneDB ID: retro_ecab_357

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:30880855..30881790(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSECAG00000008502
• Aliases: None
• Description: non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]

Sequence

>retro_ecab_357
ACTATGCCCCAATATAACCATCTCTTTATGGGGAATCTTCTTCCTGACATTGCTGAGGAGGAAATGAGGAAACTGTTTGA
GAAATATGGGAAGGCAGGCAAAGGCTTCATTCATAAGGACAAGGGCTTCATCCTTATTTGTTTGGAAACATAAAGCCTAG
CAGAGATTGCCAGAGTGGAGTTGGACAACATGCTACTCCATGGAAAGCAGCTAAATGTATGCTTGGCTGGCCATAGTACA
TCCCTTATGTTCTGAAACCTTCCTCAGTATGTGTCCAACAACTGCTGAAGGAAGCCTTTTCTGTATTGGGCAGGTGGAGA
GGGCTATAATCATAATGCATGATTGAGGAAGGTCCTCAGGAAAAGGCAAGGTTGAGTTCTCAGGGAAGCCATCTGCTGGC
AAAACTCTGGACAGATGCAGTGAAGGCTCCTGACTGCTAACCACATTTCCTCAGCCTGTGACTATGGAGCCCATGGACCA
GTTAGATGATGAAGAGGGATTTCCAGAGAAGCTGGTTATAAAGAACTAGCAATTTCACAAGGAGTGAGAACGGCCACCCA
GATTTGCACAGCCTGGCTCTTTTGAGTATGAGTATGCCAATGTGATGGAAGGCATTCAATGAGATAGAGAAGCAGCAGCA
GGAGCAAGTGGACCTCAACATCAAGAAAGCTCATGGCAAACTGGAGATGGAGATGGAGGCTGCCCACTACAAGCACCAGG
TCATGCTAATGAGGCAGGATTTGATGAGGCTTCAAGAACTTCAGAGGATGAATGAGCTGCACAACCAAGACGTGCAAAAA
CAAAAGCAGTTGGAGCTCAGGCAGGAGGAGGAGTACAGGTGTCATGAGGAAGAGCTGCAGCGGCAACAGGAAAAAATGAT
GCAATGACAGGAGGAGGGATTCAACGGGACCTTCCGTGATGCTAGAGATATGGAG

Alignment

ORF - retro_ecab_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 66.6 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQ
          T..Q...LF.GNL.PDI.EEEMRKLFEKYGKAG..FIHKDKGF..I.LET..LAEIA.VELDNM.L.GKQ
Retrocopy TMPQYNHLFMGNLLPDIAEEEMRKLFEKYGKAGKGFIHKDKGFILICLET*SLAEIARVELDNMLLHGKQ

Parental  LRVRFACHSASLTVRNLPQYVSN-ELLEEAFSVFG-QVERAVVIVDDRGRPSGKGIVEFSGKPAARKALD
          L.V..A.HS.SL...NLPQYVSN..LL.EAFSV.G.QVERA..I..D.GR.SGKG.VEFSGKP.A.K.LD
Retrocopy LNVCLAGHSTSLMF*NLPQYVSN<QLLKEAFSVLG<QVERAIIIMHD*GRSSGKGKVEFSGKPSAGKTLD

Parental  RCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYA-MRWKALI
          RCSEGS.LLTTFP.PVT.EPMDQLDDEEG.PEKLVIKN.QFHKE.E.PPRFAQPGSFEYEYA.M.WKA..
Retrocopy RCSEGS*LLTTFPQPVTMEPMDQLDDEEGFPEKLVIKN*QFHKE*ERPPRFAQPGSFEYEYA>M*WKAFN

Parental  EMEKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQE
          E.EKQQQ.QVD.NIK.A..KLEMEMEAA...HQVMLMRQDLMR.Q.EL.RM.ELHNQ.VQK.KQLELRQE
Retrocopy EIEKQQQEQVDLNIKKAHGKLEMEMEAAHYKHQVMLMRQDLMRLQ-ELQRMNELHNQDVQKQKQLELRQE

Parental  EERRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQE
          EE.R..EEE..RQQE.MM..Q.EGF.GTF.DAR..E
Retrocopy EEYRCHEEELQRQQEKMMQ*QEEGFNGTFRDARDME

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	96.87 RPM
SRP021940_cerebellum	0.00 RPM	234.47 RPM
SRP021940_embryo	0.03 RPM	573.37 RPM
SRP021940_placental_villous	0.00 RPM	159.01 RPM
SRP021940_synovial_membrane	0.00 RPM	189.47 RPM
SRP021940_testis	0.00 RPM	81.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_357 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_357 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357 , retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,