RetrogeneDB ID: retro_btau_1659

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:89167048..89168069(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.26664
• Ensembl ID: ENSBTAG00000017550
• Aliases: None
• Description: Casein kinase I isoform gamma-3 [Source:UniProtKB/Swiss-Prot;Acc:P35509]

Sequence

>retro_btau_1659
AACACTCAAGGAACTGGTTCTTCGTCCTCTGGAATTTTAATGGTTGGATCTAACTTTAGAGTTGGGAAAAAAAACTGGAT
ATGGGAATTTTGGAGAACTACAATTAGGAAAAAATTTGTATACAAATGAATATATGGCCATTAAATTGGAGCTCATGAAA
TCCAGAGCATCACAGCTACATTTGACTGTATTCCAATTTCTACAAGCAGTTAGGATCTGGAGATGGTATACCTCAAGTTT
ATTATTTTGGCCCTTGTGGTAAATACAGCACTATGGTGATAGAACTGCTGGGACCTATTTTGCAAGATTTGTTTGATTTG
TGTGACAGAACATTTTCTCTTAAAACTATTCTCATGATAGCTATCTAACTGATTTCTCACATGCAATATGTCCATTCAAA
GAACTTGATATACAGAGATGTAAAACCTGAGAACTGTTTAATAGGCTGTCTGGGAAACAAAACACAGCAAGTTATTCATA
TTATAGATTTTGGTTTGGCAAAGGAATATACTGATCCAGAGACAAAGAAACACATACCATACAAAGAGCACAAAAGCCTT
ATAGGAACAGCTATATATATGAGCACAAACACACATTTAGGGAAAGAACAAAGTAGAAGAGATGACTTAGAAGCTTTAGG
TCACATGTTCATGTATTTTCTGAGAGGCAGTCTTCCTTGGCAAGGTTTAAAAGCTGACACATTAAAAAAGCAATATCAGA
AAATTGGAGATACGAAACGAGCCACACCAATAGAAGTGTAATGTGAAAATTTTCCAGAAGAAATGGCAATGTATCTTTGT
TATGTAAGAAGGCTAGATTTTTTTGAAAAACCAGATTATGACTACCTAAGAAGGCTTTTTACTGACTTGTTTGATGGAAA
AGGATATATGTTGATTATGAATATGACTGGATTGGTAAATAGTTGCCTACTCTAGTGGGTCCATTCAGCAAGATCCTGCT
CTGTATATCAATCAGAGGAGCACATCCACATGGAGATAAGATACAATCCCAAAATCAGGTT

Alignment

ORF - retro_btau_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 80.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NTRGTGSSSSGVLMVGPNFRVGKKI-GCGNFGELRLGKNLYTNEYVAIKLEPMKSRAPQLHLE-YRF-YK
          NT.GTGSSSSG.LMVG.NFRVG....G.GNFGEL.LGKNLYTNEY.AIKLE.MKSRA.QLHL....F.YK
Retrocopy NTQGTGSSSSGILMVGSNFRVGXXX>GYGNFGELQLGKNLYTNEYMAIKLELMKSRASQLHLTVFQF>YK

Parental  QLGSGDGIPQVYYFGPCGKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYR
          QLGSGDGIPQVYYFGPCGKY..MV.ELLGP.L.DLFDLCDRTFSLKT.LMIAI.LIS.M.YVHSKNLIYR
Retrocopy QLGSGDGIPQVYYFGPCGKYSTMVIELLGPILQDLFDLCDRTFSLKTILMIAI*LISHMQYVHSKNLIYR

Parental  DVKPENFLIGRPGNKTQQVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDD
          DVKPEN.LIG..GNKTQQVIHIIDFGLAKEY.DPETKKHIPY.EHKSL.GTA.YMS.NTHLGKEQSRRDD
Retrocopy DVKPENCLIGCLGNKTQQVIHIIDFGLAKEYTDPETKKHIPYKEHKSLIGTAIYMSTNTHLGKEQSRRDD

Parental  LEALGHMFMYFLRGSLPWQGLKADTLKERYQKIGDTKRATPIEVLCENFP-EMATYLRYVRRLDFFEKPD
          LEALGHMFMYFLRGSLPWQGLKADTLK..YQKIGDTKRATPIEV.CENFP.EMA.YL.YVRRLDFFEKPD
Retrocopy LEALGHMFMYFLRGSLPWQGLKADTLKKQYQKIGDTKRATPIEV*CENFPEEMAMYLCYVRRLDFFEKPD

Parental  YDYLRKLFTDLFDRKGYMF-DYEYDWIGKQLPTPV-GAVQQDPALSSN-REAHPHRDKIQSKNQV
          YDYLR.LFTDLFD.KGYM..DYEYDWIGK.LPT.V.G..QQDPAL..N.R.AHPH.DKIQS.NQV
Retrocopy YDYLRRLFTDLFDGKGYML<DYEYDWIGK*LPTLV<GSIQQDPALYIN>RGAHPHGDKIQSQNQV

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	19.32 RPM
ERP005899_muscle	0.00 RPM	22.33 RPM
SRP017611_brain	0.00 RPM	19.55 RPM
SRP017611_kidney	0.00 RPM	26.02 RPM
SRP017611_liver	0.00 RPM	9.06 RPM
SRP030211_testis	0.00 RPM	13.34 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1659 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Bos taurus	ENSBTAG00000017550	1 retrocopy	retro_btau_1659 ,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695, retro_cjac_3279,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189,