RetrogeneDB ID: retro_btau_1188

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:17924841..17925513(-)
• Located in intron of: ENSBTAG00000012944

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSBTAG00000001440
• Aliases: None
• Description: Phosphomannomutase 2 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZJ9]

Sequence

>retro_btau_1188
AAAATTACCAAAGACATGGATTGCTTTCTGCAAAAACTGAGGCAGAAGATCAAAATTGGTGTCGTCGGCGGGTCGGACTT
TGAGAAAGTACAGGAGCAGCTGGGAGATGACGTTATTAAAAAATATGATTACGTGTTTCCAGAAAATGGCTTGGTAGCAT
ACAGAGATGGGAAACTCTTGTGTAAACAGAATATTCAAGGTCACCTGGGTGAAGCCCTAATCCAGGATTTAATCAACTAC
TGTCTGAGCTACATCGCGAAAATCAAGCTCCCGAAGAAGAGGGGCACTTTCATAGAGTTCCGTAACGGGATGCTGAACGT
GTCGCCGATCTGAAGAAGCTGCAGCCAGGAAGAACGCATTGAGTTCTACGAGCTCGATCGGAAAGAAAACATAAGACAAA
AGTTCGTGGAGGATCTGCGAAAAGAGTTTGCTGGGAAAGGCCTCACGTTTTCCATAAGAGGCCAGATCAGCTTCGATGTC
TTCCCCGATGGCTGGGACAAGAGGTACTGCCTGGGACACGTGGAAAAGGACGGCTATAAGACCATCTATTTCTTCGGCGA
CAAAACCATGCCAGGCGGGAATGACCACGAGATCTTCACAGACCCCAGGACAGTGGGCTACACGGTGGCGGCGCCGGAGG
ACACGCGCAGGATCTGCGAGGAGCTCTTCTGC

Alignment

ORF - retro_btau_1188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.66 %
• Parental protein coverage: 91.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KITKDMDCFLQKLRQKIKIGVVGGSDFEKVQEQLGDDVIKKYDYVFPENGLVAYRDGKLLCKQNIQGHLG
          KITKDMDCFLQKLRQKIKIGVVGGSDFEKVQEQLGDDVIKKYDYVFPENGLVAYRDGKLLCKQNIQGHLG
Retrocopy KITKDMDCFLQKLRQKIKIGVVGGSDFEKVQEQLGDDVIKKYDYVFPENGLVAYRDGKLLCKQNIQGHLG

Parental  EALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPIGRSCSQEERIEFYELDQKENIRQKFVEDLR
          EALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPI.RSCSQEERIEFYELD.KENIRQKFVEDLR
Retrocopy EALIQDLINYCLSYIAKIKLPKKRGTFIEFRNGMLNVSPI*RSCSQEERIEFYELDRKENIRQKFVEDLR

Parental  KEFAGKGLTFSIGGQISFDVFPDGWDKRYCLGHVEKDGYKTIYFFGDKTMPGGNDHEIFTDPRTVGYTVA
          KEFAGKGLTFSI.GQISFDVFPDGWDKRYCLGHVEKDGYKTIYFFGDKTMPGGNDHEIFTDPRTVGYTVA
Retrocopy KEFAGKGLTFSIRGQISFDVFPDGWDKRYCLGHVEKDGYKTIYFFGDKTMPGGNDHEIFTDPRTVGYTVA

Parental  APEDTRRICEELFC
          APEDTRRICEELFC
Retrocopy APEDTRRICEELFC

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	14.13 RPM
ERP005899_muscle	0.63 RPM	53.58 RPM
SRP017611_brain	0.23 RPM	8.13 RPM
SRP017611_kidney	0.12 RPM	25.96 RPM
SRP017611_liver	0.91 RPM	32.70 RPM
SRP030211_testis	0.14 RPM	18.99 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1188 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001440	2 retrocopies	retro_btau_1188 , retro_btau_307,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329,
Tursiops truncatus	ENSTTRG00000014827	2 retrocopies	retro_ttru_1894, retro_ttru_977,