RetrogeneDB ID: retro_btau_838

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:119666467..119666810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSBTAG00000002944
• Aliases: None
• Description: ATP synthase lipid-binding protein, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q3ZC75]

Sequence

>retro_btau_838
AGCCAGGCAAGCTGTTTGCCTGCACCGCCACTGCAAGCTGGATCCAGAGTTGCAGGCAGACCAATTTCTGCATCAGTATT
ATCTCGACTGAAGGCTAGGACTGCAGAGGGCTCTGCGGTATTTAGTGGGGCCCAGAATGGTGTGTCTCAGTTAATCCAGA
GGGAGTTCAGACCAGTGCAGTCAGCAGAGATGCTGAGACTGCGGCCACTTTTATTGGTGCACTTGTGCAACAACAGGAGT
GGCTGGTTCCAGTGCTGGTATTGGAACAGTCTTCGGCAGCCTCATCATTGATTATGCCAGAAACCCTTTTCTGAAGCAGC
AACTATTCTCATATGCTATCCTG

Alignment

ORF - retro_btau_838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 80.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKLACTPAL-IRAGSRVAYRPISASVLSRPETRTGEGCTVFNGTQNGVSQLIQREF-QTTAVNRDIDTAA
          ....C.PA....AGSRVA.RPISASVLSR...RT.EG..VF.G.QNGVSQLIQREF.QT.AV.RD..TAA
Retrocopy SQASCLPAPPLQAGSRVAGRPISASVLSRLKARTAEGSAVFSGAQNGVSQLIQREF<QTSAVSRDAETAA

Parental  KFIGA-GAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAIL
          .FIGA...AT.GVAGS.AGIGTVFGSLII.YARNP.LKQQLFSYAIL
Retrocopy TFIGA<TCATTGVAGSSAGIGTVFGSLIIDYARNPFLKQQLFSYAIL

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	56.52 RPM	60.92 RPM
ERP005899_muscle	3.33 RPM	231.64 RPM
SRP017611_brain	12.52 RPM	59.57 RPM
SRP017611_kidney	1.07 RPM	216.34 RPM
SRP017611_liver	29.07 RPM	51.57 RPM
SRP030211_testis	0.51 RPM	25.89 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_838 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_838 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002944	1 retrocopy	retro_btau_838 ,
Bos taurus	ENSBTAG00000005735	11 retrocopies	retro_btau_1405, retro_btau_1414, retro_btau_733, retro_btau_734, retro_btau_735, retro_btau_737, retro_btau_739, retro_btau_740, retro_btau_741, retro_btau_742, retro_btau_994,
Bos taurus	ENSBTAG00000018339	3 retrocopies	retro_btau_1506, retro_btau_423, retro_btau_431,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,
Tursiops truncatus	ENSTTRG00000011524	3 retrocopies	retro_ttru_268, retro_ttru_510, retro_ttru_588,