RetrogeneDB ID: retro_btau_1408

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:10994577..10995123(-)
• Located in intron of: ENSBTAG00000003036

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.48915
• Ensembl ID: ENSBTAG00000014343
• Aliases: None
• Description: rab-like protein 5 [Source:RefSeq peptide;Acc:NP_001015612]

Sequence

>retro_btau_1408
TTGCTGAAGGCCAGAGTCCTCCTTGGGGGCCCCTGCGAGAGTGGAAAAACCATTTTGGCCTACTTTCTGACACAAGCTTC
TGATATCACTGAATACAACCCAACCCAAGGAGTGAGGATCCTGGAATTTGAGAATCCACGTGTTACCAGCAAACAACGAA
GGCGCGGGTGTGAATTTGAGCTCTGGGATTGTGGTGGTGATCCAGAGTTCGAGTCTTACTGGCCAGCCCTGATGAAGGAC
TCTCATGGGGTGGTGATCGTCTTCAATGCCAGCATCCTAAGTCACCTGAAGGAAATTGAGATGTGGTATTCCTGTTTCGT
TCAGCAGCAGTTCTTACAGAATACTCCGTGTCTGTTAATTGCACACCACACACCAGGCTCCAGAAGTGACAAAGAAAACC
CAGCTCTGGCACCACCCTTGAACAAGCTGAAGCTGGTGCACTCGAATCTTGAGGACTACCCGGAAGAGATCAGGATGGAA
TTCATCCAGTATTTAAGAAGCATAATCAACTTAGTGTCCGAGAGCAGAGACCCGGAGGAGATATCC

Alignment

ORF - retro_btau_1408 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.52 %
• Parental protein coverage: 98.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLKAKILFVGPCESGKTVLANFLTESSDITEYNPTQGVRILEFENPHVTSNNKGTGCEFELWDCGGDPKF
          .LKA..L..GPCESGKT.LA.FLT..SDITEYNPTQGVRILEFENP.VTS.....GCEFELWDCGGDP.F
Retrocopy LLKARVLLGGPCESGKTILAYFLTQASDITEYNPTQGVRILEFENPRVTSKQRRRGCEFELWDCGGDPEF

Parental  ESCWPALMKDSHGVVIVFNADIPSHLKEIETWYSCFVQQQFLQNTQCLLIAHHKPGSGSDKDNPTLAPPL
          ES.WPALMKDSHGVVIVFNA.I.SHLKEIE.WYSCFVQQQFLQNT.CLLIAHH.PGS.SDK.NP.LAPPL
Retrocopy ESYWPALMKDSHGVVIVFNASILSHLKEIEMWYSCFVQQQFLQNTPCLLIAHHTPGSRSDKENPALAPPL

Parental  NKLKLVHSNLEDDPEEIRMEFIKYLRSIINSVSESRDREEMS
          NKLKLVHSNLED.PEEIRMEFI.YLRSIIN.VSESRD.EE.S
Retrocopy NKLKLVHSNLEDYPEEIRMEFIQYLRSIINLVSESRDPEEIS

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	3.39 RPM
ERP005899_muscle	0.00 RPM	3.38 RPM
SRP017611_brain	0.05 RPM	21.24 RPM
SRP017611_kidney	0.00 RPM	12.27 RPM
SRP017611_liver	0.00 RPM	2.11 RPM
SRP030211_testis	0.02 RPM	47.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1408 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014343	1 retrocopy	retro_btau_1408 ,
Choloepus hoffmanni	ENSCHOG00000012225	1 retrocopy	retro_chof_409,
Macropus eugenii	ENSMEUG00000006225	1 retrocopy	retro_meug_331,
Myotis lucifugus	ENSMLUG00000012634	1 retrocopy	retro_mluc_2510,
Oryctolagus cuniculus	ENSOCUG00000007709	1 retrocopy	retro_ocun_522,
Tursiops truncatus	ENSTTRG00000005871	1 retrocopy	retro_ttru_110,