RetrogeneDB ID: retro_ecab_427

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:14406043..14407398(+)
• 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_427
ATGCGGAGCAATAAAACCTTTAACTTGGAGAAGCAGAACCATACTCCAAGGAAGCATCATCAGCATCACCACCAGCAGCC
ACCACCGCCACGACCAATACCTGCAAATGGTCAACAAGCCAGCAGCCAAAATGAAGGCTTGACTATTGACCTGAAGAATT
TTAGGAAACCAGGAGAGATGACCTTCACCCAACGTATCCGGCTCTTTGTTGGCAATTTTCCTTCTGACATCACTGAGGAG
GAAATGAGGAAATTATTTGAGAAACATGGGAAGGCAGGCGAAGTCTTCATTCATAAGGATAAGGGCTTTGCCTTATCAGC
TTGGAAACATGGGAGATTGCCAAAGTGGAGCTGGACAACATGCCACTCCAGGGAAAGCAGCTCTGTGTGTGCCTTGCCTG
CCATAGCGGATCCCTTGCTGTCTGAAACCTTCCTTAGTATGTATCCAACGATCTGCCAGAGGAAGCCTTTTCTGTGTCCG
TCCAGGTGGAGAGGGCTATAGTTGTTGTGGATGATCGAGGAAGGCCCTCAGGAAAAGGCATTGTTGAATTCTCAGGGAAG
CCAGCTGCTTGGAAAGCTCTGGACAGATACAGTGAAGGCTTCTTCCTGCTAACCACATTTCCTTGGCCTGTGACTTTAGA
GCTCGTGGACCGGTTAGATGATGAAGAGGGACTTCCAGAGATTCTGGTTATAAAGAACAATCAATTTCACAATGAACAAG
AGCATCCACCCAGATTTGCACAGCCTGGCTCCTTTGAGTATGAGTATGCCATGCGCTGGAATGCACTCACTGAGGTGGAG
AAGCAGCAGCAGGATCGAGTGGACCACAATATCAAGGAAGCGCATGAGAAACTGGAGATGGAGATGCAGGCTACTTGCCA
TGAGCACCAGGTCATGCTAATGAGGCAGGATTTGATGAGGCGTCAAGAAGAACTTCAGAGGATGGAAGAGCTGCACAACC
AAGAAGTGCAAAAATGAAAGCAACTGGAGCTCAGGCAGGAGGAGGAGCACAGGTGCCGGGAGGAAGAGATGAGGCAACAA
CAGGAAGGACTCAAGGGAAGCTTGCCTGACGCAAGAGAGCAGGAGATATGACTGGACCAGTTGGCTATGGGAGGTGCTAT
GGGCATAAACAACAGAGACGCCATGCCCCCTGCTCCTGTGCCTGCTGGTACTCCAGCTCCTCCAGGACCTGCCACTATGA
TGCCAAATGGAACCTTGGGATTGACCTCACCAACAACTGAAGGCTTTGGCCAACCTGCTACAACGGAAGGAATTGGGGCA
ATTGGTGGAACCCCTCCTGCATTCAACCATGCAGCTCCTGGAGCAGAATTTGCTCCAAACAAACGTCATCGATAT

Alignment

ORF - retro_ecab_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSNKTFNLEKQNHTPRKHHQHHHQQHHQQQQQQPPPPPIPANGQQASSQNEGLTIDLKNFRKPGEKTFT
          M.SNKTFNLEKQNHTPRK....HHQ.HH...QQ.PPP.PIPANGQQASSQNEGLTIDLKNFRKPGE.TFT
Retrocopy MRSNKTFNLEKQNHTPRK----HHQHHH---QQPPPPRPIPANGQQASSQNEGLTIDLKNFRKPGEMTFT

Parental  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGF-IRLETRTLAEIAKVELDNMPLRGKQLR
          QR.RLFVGN.P.DITEEEMRKLFEK.GKAGEVFIHKDKGF...I.LET....EIAKVELDNMPL.GKQL.
Retrocopy QRIRLFVGNFPSDITEEEMRKLFEKHGKAGEVFIHKDKGFAL<ISLETW---EIAKVELDNMPLQGKQLC

Parental  VRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSE
          V..ACHS.SL.V.NLP.YVSN.L.EEAFSV..QVERA.V.VDDRGRPSGKGIVEFSGKPAA.KALDR.SE
Retrocopy VCLACHSGSLAV*NLP*YVSNDLPEEAFSVSVQVERAIVVVDDRGRPSGKGIVEFSGKPAAWKALDRYSE

Parental  GSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQ
          G.FLLTTFP.PVT.E..D.LDDEEGLPE.LVIKN.QFH.E.E.PPRFAQPGSFEYEYAMRW.AL.E.EKQ
Retrocopy GFFLLTTFPWPVTLELVDRLDDEEGLPEILVIKNNQFHNEQEHPPRFAQPGSFEYEYAMRWNALTEVEKQ

Parental  QQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRR
          QQD.VD.NIKEA.EKL..EME.....H......Q....RQ...RR.EEL..Q........E.........
Retrocopy QQDRVDHNIKEAHEKL--EMEMQATCHE----HQVMLMRQDLMRRQEEL--QRMEELHNQEVQK*KQLEL

Parental  REEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATMM
          R.EE..R..EE.MR.QQEG.KG..PDAREQEI...Q.AMGGAMGINNR.AMPPAPVPAGTPAPPGPATMM
Retrocopy RQEEEHRCREEEMRQQQEGLKGSLPDAREQEI*LDQLAMGGAMGINNRDAMPPAPVPAGTPAPPGPATMM

Parental  PDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY
          P.GTLGLT.PTTE.FGQ.AT.EGIGAIGGTPPAFN.AAPGAEFAPNKR.RY
Retrocopy PNGTLGLTSPTTEGFGQPATTEGIGAIGGTPPAFNHAAPGAEFAPNKRHRY

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	0.12 RPM	96.87 RPM
SRP021940_cerebellum	0.26 RPM	234.47 RPM
SRP021940_embryo	0.79 RPM	573.37 RPM
SRP021940_placental_villous	0.14 RPM	159.01 RPM
SRP021940_synovial_membrane	0.22 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_427 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_427 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,