RetrogeneDB ID: retro_btau_790

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:19814150..19815225(-)
• Located in intron of: ENSBTAG00000006894

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_790
GAACTCCCAGGCACTGTATCAGTGTTTGGGCTCGAGCTGTCCTGTCCTGGCAAAGTAGATTCTGAAGTTACGACACTAAA
TGCACCTCAACTTGAGAGTAACTTCAAAAAGCTTCACATCTTAGAGTTGAAACGAAGGAAAAGTTTCCATCCAGAAATTG
AGAAAGGAAAACTTCAGCCTTGGACAAAACTACTAGTGGAAGAACCCATTTATGATCCTGTACATGCAGCTCCAGCCGTG
TCTACACGTGTGTTTTATATCAGCCTAGGGGTTTGCTGTCCAGTTATATTTCTTATAGTACTAGTATTAGTTGTTTTGCA
TCTTCATAGTGTGAAAAGGATTGAACTGGGAGATAGCATCAGCGCCAGCAGTAGTTCCCAAGGGCTGTCTCAGTCCCAGT
CGTTCCCAGATGTCTCGGTATGTGAGAGGCAACACACCCAACAATACAACTCCCATCTCCCGTTATCTAACCTTGTGGCT
AGAGGAGTACAACTTGAGAAATGTCGCTCTTTTGGAGGCCAGAGCTTAGGTGAATGATATCAAAATATCTATCTAGGGAG
AGGAACTCAAAAGATGTACTCTAAGAAGGTACCTTTTGGTGTACTTCCCATGGGGTTTATGTAGATGAAAAAGATCCAGA
TAAAGAGCAACAAGCATTTGTAAAAACAGTTAGAGATCGAGCTTCTGAAATTCAGGTGACTATGATGCTCCCTGAAAGTT
GTGAGCTATGAGATCTTCATCACAGAAATCTTCCTATTAGCCACGTGTGAACAGAAGAAGGGGAAAAGCCCATGGTGGAT
TGCCTTACATGTACTGGGGGTATCTTAAATTGTTTTTATGACAGTGCGAATATGTAGAAGCCGATAGTCAGCAGGAAACT
TCTCAACAAAAGCTAGTTCACATGGCTGCTCAGATTGCCTGTGGAATGAGCTACCTGGTCAGAAAGAAGTCATCCACAAA
GACCTGGCTCCTAGGATCTCTGTCATTGATGACAACTTCAAGTTAAGAGCAAAGCCACTCCCTCTCCAGAGTCTTGTTCC
CCATGGACTCTCACTGTCTGGGGAACAACAAAAAC

Alignment

ORF - retro_btau_790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.31 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  EVPRTLSAVFRVELSCTGKVDSEVMIL-MQLNLTVNSSKNFT-VLNFKRRKMCYKKLE-EVKTSALDKNT
          E.P.T.S.VF..ELSC.GKVDSEV..L.M.LNL.V..SK.FT..L..KRRK......E.E.KTSALDK.T
Retrocopy ELPGTVS-VFGLELSCPGKVDSEVTTL>MHLNLRV-TSKSFT<ILELKRRKSFHPEIE<ERKTSALDKTT

Parental  S-RT-IYDPVHAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELDDSISASSSSQGLSQ-PS
          S.RT.IYDPVHAAP..STRVFYIS.GVCC.VIFL....L.VLHLHS.KRIEL.DSISASSSSQGLSQ.PS
Retrocopy SGRT>IYDPVHAAPAVSTRVFYISLGVCCPVIFLIVLVLVVLHLHSVKRIELGDSISASSSSQGLSQ>PS

Parental  -TQTTQYLRADTPNNATPITSSSGYPTLRIEKNDLRSVTLLEAKAKVKDIAISRERITLK-DVLQEGTFG
          ..Q...Y.R..TPNN.TPI...S.Y.TL..E...LR.V.LLEA.A.V.DI.IS.....LK.DVL.EGTF.
Retrocopy RSQMSRYVRGNTPNNTTPI---SRYLTLWLEEYNLRNVALLEARA*VNDIKISI*GEELK>DVL*EGTFW

Parental  RIFHGILVDEKDPNKEKQAFVKTVKDTDQASEIQVTMMLTESCKLRGLHHRNLLPITNVCIEEGEKPMVI
          ...HG..VDEKDP.KE.QAFVKTV...D.ASEIQVTMML.ESC.L..LHHRN.LPI..V..EEGEKPMV.
Retrocopy CTSHGVYVDEKDPDKEQQAFVKTVR--DRASEIQVTMMLPESCEL*DLHHRN-LPISHV*TEEGEKPMVD

Parental  -LPYMNWGNLKLFLRQCKLVEANNPQAISQQDLVHMAIQIACGMSYLAR-REVIHKDLAARNCVIDDT-L
          .LPYM.WG.LKLFL.QC..VEA...Q..SQQ.LVHMA.QIACGMSYL.R..EVIHKDLA.R..VIDD..L
Retrocopy <LPYMYWGYLKLFL*QCEYVEADSQQETSQQKLVHMAAQIACGMSYLVR<KEVIHKDLAPRISVIDDN<L

Parental  QVKI-TDNALSRDLFPMDYHCLGDNEN
          QVK......LSR.LFPMD.HCLG.N.N
Retrocopy QVKS<QSHSLSRVLFPMDSHCLGNNKN

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	0.00 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	0.04 RPM	26.51 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_790 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_790 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,