RetrogeneDB ID: retro_ecab_318

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:67188428..67189767(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000014403
• Aliases: None
• Description: None

Sequence

>retro_ecab_318
CGCCAGTGCAAGTTTGTCCACGTGTGGTAGGTAGAAGTCCAGATTGGTAATGCCTCCTGGGAATTGTACTGCCTTGAACT
TGGAATTTAGCCCAATGGTCAAATGCCGAGTGACAAAACCACTGCTGGTGGGGATGACTCCTTCAAGACATTCTTCGGGG
AGATTGGGGCTAGCCAGCACATGCCCAAAGCAGGGTCTGTGGACCTGGAGCCACCGCAGTCAATAGAGTGCACACGGGAC
ATATAGGCAGCTCTTCTACTCAGAGTAGATGGTCACCGGGAAGAAATATACAGCCAATAATTAGGCCAAAGGCCATTACA
TCATCGGCAAGGAGATCATTGACCTAGTCCTGGACCGGATCCAAAAACTGGCAGATTTCTGCATGGGGCTGTGAGGCTTC
CTCATCTTCCACAGCTTCAGTGCAGCACCAGCTCTGGGTTTGTGTCTCTGCTCATGAAGCAGCACTTGGTAGAATGTGGC
ACAAAGTCTAAGCTCAAATTTGCCATTTACCCAGTCTCCCATGTTTCTAAAGCCATAGTGGACCCCCTACAACTCCATCC
TGACCACTCACACAATACATAAAATTATGACTGTGCCTTCATGGTAGATAAGGAAGCCAGCTACGACATATGTGGGCACA
ACCTGGTTGTCCAATGGCCCATGTACACTGACCTCAGTTGTGGGATTGGGCAGATCATGTCCACCATCAACACCTCCCAT
CGATTTGATGGGGCCCTGAAAGTGGACTTGATGGAATTCCCAACCAACCTGGTCCCTACCCCCACATCTACTTCCCCCTG
GCTACCTATGCCTGGTCATCTCAACCAAGACTGTCTACTACAAGCAGCTGTCAGCGGCCAAGACCACCAATGCCTACTTC
TAGCTAGCAAACCAGATGGTCAAGTATGACCCTTGCCATGGGAAGTACATGCCTGCTGCATGTTGTATGGGGGGACCCGT
CCTGAAGATGTCAACGCGGCTGTCCCCACCATCGAGACCAAGCACACCATCCAGTTTGTGAATTGGAGCTCAAGTGGATT
TAAGGTGGGCATCAACTACCAGCCCCCCAGCTGTCATCCCTGGGGGAAACATGAGCAATATTCAGTGGGCCATGTGTATG
CTGGGCAACAGCACTGCCCTCACCAAGGCCTGGGCACGCCTGGACCATAAGTTCAATCTCACCTATGCAAGGTGAACATT
CGTGCCCTGATACATGGGGGAAGTCATGGAGGAAGCAGACTTCTCTGAGGTCCTGGGGGACCTGGCAGCCCTGGAGAAAG
ATTACAAAGAGGTGGGCACAGATCCCATGGAAGCAGAGGCCAGATGATGGGCAGAATAC

Alignment

ORF - retro_ecab_318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
          R.C...HV....VQIGNA.WELYCLE.GI.P.GQMPSDKT..GGDDSF.TFF.E.GA..H.P.A..VDLE
Retrocopy RQCKFVHVW*VEVQIGNASWELYCLELGI*PNGQMPSDKTTAGGDDSFKTFFGEIGASQHMPKAGSVDLE

Parental  P-TVVDEVRTG-TYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLDRIRKLADLCTGLQGFLIFH
          P.T.V..V.TG.TYRQLF..E...TGK...ANN.A.GHY.IGKEI.DLVLDRI.KLAD.C.GL.GFLIFH
Retrocopy P<TAVNRVHTG<TYRQLFYSE*MVTGKKYTANN*AKGHYIIGKEIIDLVLDRIQKLADFCMGL*GFLIFH

Parental  SFGGG-TGSGFASLLMERLSVDYGKKSKLEFAIYPAPQVSTAVVEP-YNSILTTHTTLE-HSDCAFMVDN
          SF....T.SGF.SLLM....V..G.KSKL.FAIYP...VS.A.V.P.YNSILTTHT......DCAFMVD.
Retrocopy SFSAA<TSSGFVSLLMKQHLVECGTKSKLKFAIYPVSHVSKAIVDP>YNSILTTHTIHK<NYDCAFMVDK

Parental  EAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVP-YPRIHFPLATYA-P
          EA.YDIC..NL....P.YT.L...IGQI.S.I..S.RFDGAL.VDL.EF.TNLVP.YP.I.FPLATYA..
Retrocopy EASYDICGHNLVVQWPMYTDLSCGIGQIMSTINTSHRFDGALKVDLMEFPTNLVP<YPHIYFPLATYA<L

Parental  VISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYM-ACCMLYRGDVVPKDVNAAIATIKTKRTIQF
          VIS....Y..QLS.A..TNA.F..ANQMVK.DP.HGKYM.ACCMLY.G...P.DVNAA..TI.TK.TIQF
Retrocopy VISTKTVYYKQLSAAKTTNAYF*LANQMVKYDPCHGKYM<ACCMLY-GGTRPEDVNAAVPTIETKHTIQF

Parental  VDWCPTGFKVGINYQPPT-VVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEG
          V.W...GFKVGINYQPP..V.PGG.....Q.A.CML.N.TA...AWARLDHKF.L.YA...FV..Y.GE.
Retrocopy VNWSSSGFKVGINYQPPS>VIPGGNMSNIQWAMCMLGNSTALTKAWARLDHKFNLTYAR*TFVP*YMGEV

Parental  MEEGEFSEAREDLAALEKDYEEVGVDSVEAEAEEGEEY
          MEE..FSE...DLAALEKDY.EVG.D..EAEA....EY
Retrocopy MEEADFSEVLGDLAALEKDYKEVGTDPMEAEAR*WAEY

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	0.18 RPM	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.34 RPM
SRP021940_synovial_membrane	0.03 RPM	0.00 RPM
SRP021940_testis	0.26 RPM	537.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_318 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_318 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_318 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318 ,
Equus caballus	ENSECAG00000014631	1 retrocopy	retro_ecab_147,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375, retro_fcat_647,
Monodelphis domestica	ENSMODG00000023336	1 retrocopy	retro_mdom_973,
Mustela putorius furo	ENSMPUG00000003660	1 retrocopy	retro_mputfur_130,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,