RetrogeneDB ID: retro_btau_389

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:14092293..14093148(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK38
• Ensembl ID: ENSBTAG00000011126
• Aliases: None
• Description: serine/threonine-protein kinase 38 [Source:RefSeq peptide;Acc:NP_001075071]

Sequence

>retro_btau_389
ATGGCAATGACAGGCTCAACACCTTGCTTGTCCATGAGTAGTCACACAAAGGAAAGGGTGACAATGATCAAAGTGACACT
GGAGAATTTTTATAGCAACCTTATTGCTCAACATGAAGAATGAGAAATGAGACAAAAGAAGTTAGAAAAAGTGATGGAAG
AAGAAGGCCTCAAGGCTGAAGAGAAACGACTCCGGAGATCAGCACATGCTCGGAAGGAAACAGAGTTTCTTACTTTGAAG
AGAGCAAGACTTGGACTGGAAGATTTTGAGTCCTTAAAAGTAATAGGCAGAGGAGCCTTTGGTGAGGTGTGGCTTGTTCA
GAAGAAAGATACCGGGCATGTGTATGCAATGAAAATACTTCATAAAGCACATATGCTTGAAAAAGAGCAGGTTGGCCACA
ATCGTGCAGAGCGCGACATTCTAGTGGAGGCAGACAGTTTGTGGGTTGTGAAAATGTTCTATAGTTTTCAGGATAAGCTA
AACCTCTACCTAATCATGGAGTTCCTGCCTGGAGGGGACATGATGACCCTGTTGATAAAAAAAGACAGGCTGAGAGAAGA
AGAGACTCAGTTTTACGTAGCAGAAACCGTGTTAGCCTTAGACTCTATTCACCAACTTGGGTTCATCCACAGAGACGTCA
AACAAGACAACCTTCTCCTGGACCGCAAGGGCCATGTGAAGCTTTCTGACTTTGGCCTTTACACAGGACTGAAAAAAGCA
CATAGGACAGAATTTTATAGGAATCTGAACCACAGCCTCCCCAGTGATTTCACTTTTCAGAGCATGAATTCCAAAAGGAA
AGCAGAAACCTGGAAAAGAAATAGACGTTAGCTAGCCTTCTCCAGGGTAGGCACA

Alignment

ORF - retro_btau_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.58 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMTGSTPCSSMSSHTKERVTMTKVTLENFYSNLIAQHEEREMRQKKLEKVMEEEGLKDEEKRLRRSAHA
          MAMTGSTPC.SMSSHTKERVTM.KVTLENFYSNLIAQHEE.EMRQKKLEKVMEEEGLK.EEKRLRRSAHA
Retrocopy MAMTGSTPCLSMSSHTKERVTMIKVTLENFYSNLIAQHEE*EMRQKKLEKVMEEEGLKAEEKRLRRSAHA

Parental  RKETEFLRLKRTRLGLEDFESLKVIGRGAFGEVRLVQKKDTGHVYAMKILRKADMLEKEQVGHIRAERDI
          RKETEFL.LKR.RLGLEDFESLKVIGRGAFGEV.LVQKKDTGHVYAMKIL.KA.MLEKEQVGH.RAERDI
Retrocopy RKETEFLTLKRARLGLEDFESLKVIGRGAFGEVWLVQKKDTGHVYAMKILHKAHMLEKEQVGHNRAERDI

Parental  LVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYIAETVLAIDSIHQLGFIH
          LVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLL.KKD.L.EEETQFY.AETVLA.DSIHQLGFIH
Retrocopy LVEADSLWVVKMFYSFQDKLNLYLIMEFLPGGDMMTLLIKKDRLREEETQFYVAETVLALDSIHQLGFIH

Parental  RDIKPDNLLLDSKGHVKLSDFGLCTGLKKALRTEFYRNLNHSLPCDFTFQNMNSKRKAETWKRNRRQLAF
          RD.K.DNLLLD.KGHVKLSDFGL.TGLKKA.RTEFYRNLNHSLP.DFTFQ.MNSKRKAETWKRNRR.LAF
Retrocopy RDVKQDNLLLDRKGHVKLSDFGLYTGLKKAHRTEFYRNLNHSLPSDFTFQSMNSKRKAETWKRNRR*LAF

Parental  STVGT
          S.VGT
Retrocopy SRVGT

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	19.97 RPM
ERP005899_muscle	0.16 RPM	24.60 RPM
SRP017611_brain	0.00 RPM	14.71 RPM
SRP017611_kidney	0.00 RPM	32.48 RPM
SRP017611_liver	0.00 RPM	12.84 RPM
SRP030211_testis	0.26 RPM	44.16 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_389 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011126	1 retrocopy	retro_btau_389 ,
Callithrix jacchus	ENSCJAG00000016045	2 retrocopies	retro_cjac_2806, retro_cjac_2824,
Tarsius syrichta	ENSTSYG00000012409	2 retrocopies	retro_tsyr_1276, retro_tsyr_1603,