RetrogeneDB ID: retro_btau_1256

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:15032950..15033379(-)
• Located in intron of: ENSBTAG00000020356

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLPH3L
• Ensembl ID: ENSBTAG00000020357
• Aliases: None
• Description: Golgi phosphoprotein 3-like [Source:UniProtKB/Swiss-Prot;Acc:A6H7F6]

Sequence

>retro_btau_1256
ATGACCACCTTAACTCACAGGGCCCGTCGCACTGAGGTAGGGAAGAATTCTGAAAAGAAGGTAGAAAGTGAGGAAAACAT
GAATCAAAACCGAAATCAAGACAATGAGGACACTGGAGACTCTAAGGATATCCGCCTCACCCTTATGGAAGAAGTATTGC
TCCTGGGACTAAAAGATAAAGAAGGTTACACATTTTTCTGGAACGACTGCATATCATCTGGCCCGCAAGGCGGCATCCTG
ATAGAGCCGGCCATGTGAGGTCGAATCTATCTAGAACCCCCAACCATGTGTAAGAAGCAACTACTAGACAGAAAGGTACT
GCTAAAGTCAGATAGCCCAATGGGTGATGTTTTAGTGGATGAAACTCTCAAACACATCAAAGCAACTGAACCCACAGAAA
CTGTCCAAACACGGATAGAGCTACTCACC

Alignment

ORF - retro_btau_1256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 50.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTLTHRARRTEVGKNSEKKVESEENVNQDRNQDNEDIGDSKDIRLTLMEEVLLLGLKDKEGYTSFWNDC
          MTTLTHRARRTEVGKNSEKKVESEEN.NQ.RNQDNED.GDSKDIRLTLMEEVLLLGLKDKEGYT.FWNDC
Retrocopy MTTLTHRARRTEVGKNSEKKVESEENMNQNRNQDNEDTGDSKDIRLTLMEEVLLLGLKDKEGYTFFWNDC

Parental  ISSGLRGGILIELAMRGRIYLEPPTMRKKRLLDRKVLLKSDSPTGDVLLDETLKHIKATEPTETVQTWIE
          ISSG..GGILIE.AM.GRIYLEPPTM.KK.LLDRKVLLKSDSP.GDVL.DETLKHIKATEPTETVQT.IE
Retrocopy ISSGPQGGILIEPAM*GRIYLEPPTMCKKQLLDRKVLLKSDSPMGDVLVDETLKHIKATEPTETVQTRIE

Parental  LLT
          LLT
Retrocopy LLT

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	0.07 RPM	21.34 RPM
ERP005899_muscle	0.16 RPM	72.22 RPM
SRP017611_brain	0.14 RPM	15.76 RPM
SRP017611_kidney	0.71 RPM	36.16 RPM
SRP017611_liver	0.30 RPM	33.75 RPM
SRP030211_testis	0.07 RPM	19.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1256 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1256 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	ENSBTAG00000020357	1 retrocopy	retro_btau_1256 ,
Choloepus hoffmanni	ENSCHOG00000013505	2 retrocopies	retro_chof_1173, retro_chof_1603,
Myotis lucifugus	ENSMLUG00000003484	1 retrocopy	retro_mluc_1551,
Rattus norvegicus	ENSRNOG00000047620	1 retrocopy	retro_rnor_2682,