RetrogeneDB ID: retro_btau_348

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:67566473..67567186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.101768
• Ensembl ID: ENSBTAG00000013367
• Aliases: PPT1, CLN1
• Description: palmitoyl-protein thioesterase 1 precursor [Source:RefSeq peptide;Acc:NP_776579]

Sequence

>retro_btau_348
TGGCATGGGATGGGAGATAGCTGTTGTAATCCCTTAGGCATGGGTGATATTTTAAAAAATGGTTGAGAAGAAAATACCTG
AAATTTATGTCTTATCTTTAGGGATTGGTAAGACGCTGATAGAGGATGTGGTGAACGGCTTCTTTTTGAATCTTGGCTTC
CCAGTAACAACAATTGGCAAGATTCTTGCTAAAGATCCTAGGTTTCAGTAGGGCTACAATGCTATTGGATCCTCCCAGGG
AGGCCAATTTCTATGGGCAGTGTCTCAGAGATGCCCATCACCTCCCATGAGCAATCTCATCTCAGCTGGGGGACAACGTC
AAGGTGTTTTTAGACTTCCTCGGTGCCTGGGAGGAAGCGCTCACATCTATGACTTGATCAGAAAAACACTGGATGTTGGG
CTTACAGACAAAGCTGTGCCAGCACGCCTGGTGCAAGCAGATACTGGCACAAGCCCGAAAAGGAGGCCAGGTACCACAAC
CAGAGCATCTTCTGGGCAGATATTAATCAGGGAGAGGCGTCACTGAGTCCTCCAAGAAGAACCTGATGGCCCTGAAGAAG
TTTGTGACGGTGAAATTCCTCAATAATTCCACTGTGGACCCCATGGATTCTGAGGAGTTTGGATTTTACAGAAGTGGCCA
AGCCAAGAAAACCATTCCCTCACAGGAGAGCGCCCTATACACAGAGGACTGCCTGGGGCTAAAGGCAATGGAA

Alignment

ORF - retro_btau_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.78 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WHGMGDSCCNPLSMGAIK-KMVEKKIPGIHVLSLEIGKTLREDVENSFFLNVNSQVTTVCQILAKDPKLQ
          WHGMGDSCCNPL.MG.I..KMVEKKIP.I.VLSL.IGKTL.EDV.N.FFLN....VTT...ILAKDP..Q
Retrocopy WHGMGDSCCNPLGMGDIL>KMVEKKIPEIYVLSLGIGKTLIEDVVNGFFLNLGFPVTTIGKILAKDPRFQ

Parental  QGYNAMGFSQGGQFLRAVAQRCPSPPMVNLISVGGQHQGVFGLPRCPGESSHICDFIRKTLNAGAYNKAI
          .GYNA.G.SQGGQFL.AV.QRCPSPPM.NLIS.GGQ.QGVF.LPRC.G.S.HI.D.IRKTL..G...KA.
Retrocopy *GYNAIGSSQGGQFLWAVSQRCPSPPMSNLISAGGQRQGVFRLPRCLGGSAHIYDLIRKTLDVGLTDKAV

Parental  QECLVQAE-YWHDPIREDIYRNHSIFLADINQ-ERGVNESYKKNLMALKKFVMVKFLNDTIVDPVDSEWF
          ...LVQA..YWH.P..E..Y.N.SIF.ADINQ..RGV.ES.KKNLMALKKFV.VKFLN...VDP.DSE.F
Retrocopy PARLVQAD<YWHKPEKEARYHNQSIFWADINQ<GRGVTESSKKNLMALKKFVTVKFLNNSTVDPMDSEEF

Parental  GFYRSGQAKETIPLQESTLYTQDRLGLKAMD
          GFYRSGQAK.TIP.QES.LYT.D.LGLKAM.
Retrocopy GFYRSGQAKKTIPSQESALYTEDCLGLKAME

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	28.77 RPM
ERP005899_muscle	0.00 RPM	72.22 RPM
SRP017611_brain	0.00 RPM	69.39 RPM
SRP017611_kidney	0.00 RPM	49.97 RPM
SRP017611_liver	0.00 RPM	20.39 RPM
SRP030211_testis	0.00 RPM	30.95 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_348 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_348 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013367	1 retrocopy	retro_btau_348 ,
Canis familiaris	ENSCAFG00000003004	1 retrocopy	retro_cfam_1985,
Loxodonta africana	ENSLAFG00000022663	2 retrocopies	retro_lafr_199, retro_lafr_422,
Procavia capensis	ENSPCAG00000002429	1 retrocopy	retro_pcap_94,
Tursiops truncatus	ENSTTRG00000004339	1 retrocopy	retro_ttru_659,