RetrogeneDB ID: retro_btau_793

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:24779961..24781089(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RYK
• Ensembl ID: ENSBTAG00000016999
• Aliases: None
• Description: None

Sequence

>retro_btau_793
GAACTCCCAGGCACTGTATCAGTGTTTGGGCTCGAGCTGTCCTGTCCTGGCAAAGTAGATTCTGAAGTTACGACACTAAA
TGCACCTCAACTTGACAGTAACTTCAAAAAGCTTCACAGTCTTAGAGTTGAATGAAGGAAAAGTTGCCATCCAGAAATTG
AGGTAGGAAAACTTCAGCCTTGGACAAAACCACTATCAGAAGAACCCATTTATGATCCTGTACATGCAGCCTTGTCTACA
GCCATGTCTACAGGTGTGTTTTATATCAGCCTAGGGATTTGCTGTCCAGGTATATTTCTTGTAGTACTAGTATTAGCTGT
TTTGCATCTTCATAGTGTGAAAAGGATTGAACTGGGAGATAGCATCAGCACCAGCAGTAGTTCCCAAGGGCTGTCTCAGT
CCCAGTCGTTCCCAGATGTCTCAGTATGTGAGAGGCAACACACCCAACAATACAGCTCCCATCTCCCGTTATCCAACCTT
GTGGCTAGAGGAGTACAACTTGAAAAGTGTCGCTCTTTTGGAGGCCAGAGCTTAGGTGAATGATACCAAAATATCTATCC
AGGGAGAGGAACTCAAAAGATATACTCTAAGAAGGTACCTTTTGGTGTACTTCCCATGGGGTTTATGTAGATGAATAATA
TCCAGATAAAGAGCAACAAGCATTTGTAAAAACAGTTAGAGATCAAGCTTCTGAAATTCAGGTGACCACCATGCTCCCTA
AAAGTTGTGAGCTACAAGATCACAGAAATCTTCCTATTAGCCATGTATGAACATAAGAAGGGGAAAAGCCCATGGTGGAT
TGCCTTACATGAATTGGGGGTATCTTAAATTGTTTTTATGACAGTGCAAATATGTAGAGGCAAATAGTCAGCAGGAAACT
TCTCAACAAAAGCTAGTTCACATGGCTGTTCAGATTGCCTGTGGAATGAGCTACCTGGTCAGAAGAGAAGTCTTCCACAA
AGACCTGGCTCCTAGAATCTCTGTCATTGATGACAACTTCATGTTAAGAGCAAAGCCAATCCCTCTCCAGAGTCTTGTTC
CCCATGGACTCTCACTGTCTGGGGAACAACAAAAACACGGGATCGATGGATGGCTTTTGAAAGTCTGGTTAATAATGAGT
TCTCCAGC

Alignment

ORF - retro_btau_793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.48 %
• Parental protein coverage: 65.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  EVPRTLSAVFRVELSCTGKVDSEVMIL-MQLNLTVNSSKNFTVLNFKR-RKMCYKKLEEVK-TSALDKNT
          E.P.T.S.VF..ELSC.GKVDSEV..L.M.LNLTV..SK.FTVL.....RK.C....E..K.TSALDK.T
Retrocopy ELPGTVS-VFGLELSCPGKVDSEVTTL>MHLNLTV-TSKSFTVLELNE<RKSCHPEIEVGK<TSALDKTT

Parental  -SRT-IYDPVHAAPTT--STRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELDDSISASSSSQGLSQ-
          ..RT.IYDPVHAA..T..ST.VFYIS.G.CC..IFLV...LAVLHLHS.KRIEL.DSIS.SSSSQGLSQ.
Retrocopy IRRT>IYDPVHAALSTAMSTGVFYISLGICCPGIFLVVLVLAVLHLHSVKRIELGDSISTSSSSQGLSQ>

Parental  PS-TQTTQYLRADTPNNATPITSSSGYPTLRIEKNDLRSVTLLEAKAKVKDIAISRERITLK-DVLQEGT
          PS..Q..QY.R..TPNN..PI...S.YPTL..E...L.SV.LLEA.A.V.D..IS.....LK.D.L.EGT
Retrocopy PSRSQMSQYVRGNTPNNTAPI---SRYPTLWLEEYNLKSVALLEARA*VNDTKISIQGEELK>DIL*EGT

Parental  FGRIFHGILVDEKDPNKEKQAFVKTVKDTDQASEIQVTMMLTESCKLRGLHHRNLLPITNVCIEEGEKPM
          F....HG..VDE..P.KE.QAFVKTV.D..QASEIQVT.ML..SC.L....HRNL.PI..V...EGEKPM
Retrocopy FWCTSHGVYVDE*YPDKEQQAFVKTVRD--QASEIQVTTMLPKSCELQD--HRNL-PISHV*T*EGEKPM

Parental  VI-LPYMNWGNLKLFLRQCKLVEANNPQAISQQDLVHMAIQIACGMSYLARREVIHKDLAARNCVIDDT-
          V..LPYMNWG.LKLFL.QCK.VEAN..Q..SQQ.LVHMA.QIACGMSYL.RREV.HKDLA.R..VIDD..
Retrocopy VD<LPYMNWGYLKLFL*QCKYVEANSQQETSQQKLVHMAVQIACGMSYLVRREVFHKDLAPRISVIDDN<

Parental  LQVKITDN-ALSRDLFPMDYHCL-GDNENRPVRWMALESLVNNEFSS
          L.VK...N..LSR.LFPMD.HCL.G....R..RWMA.ESLVNNEFSS
Retrocopy LHVKSKAN<SLSRVLFPMDSHCL>GTTKTRD-RWMAFESLVNNEFSS

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
ERP005899_liver	0.22 RPM	18.10 RPM
ERP005899_muscle	0.00 RPM	23.49 RPM
SRP017611_brain	0.00 RPM	12.61 RPM
SRP017611_kidney	0.00 RPM	36.33 RPM
SRP017611_liver	0.00 RPM	19.93 RPM
SRP030211_testis	0.12 RPM	26.51 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_793 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_793 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016999	2 retrocopies	retro_btau_790, retro_btau_793 ,
Loxodonta africana	ENSLAFG00000016402	1 retrocopy	retro_lafr_333,
Microcebus murinus	ENSMICG00000004507	1 retrocopy	retro_mmur_276,
Tursiops truncatus	ENSTTRG00000003760	1 retrocopy	retro_ttru_44,