RetrogeneDB ID: retro_ptro_2061

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:73623334..73624414(-)
• Located in intron of: ENSPTRG00000016079

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRD9
• Ensembl ID: ENSPTRG00000016688
• Aliases: None
• Description: bromodomain containing 9 [Source:HGNC Symbol;Acc:25818]

Sequence

>retro_ptro_2061
AGCAAACAGGCAGCTCTTTTGGGCAATGAAGAGACAGCTGTTGAGGAACCTGTCCCTGAAGTTGTACCAGTACAAGTAGA
AACTGCCAAGACATCCAAAAAGCCGAGTAGAGAAGTTATCAGCTGCATGTTTGAGCCTGAAGGGAACGCCTGCAGCTTGA
CGGACAGTACCACAGAGGAGCACGTGCTGGCGCTGGTGGAGCACGCAGCTGATGAAGCTCGGGACAGGATCAACCGGTTC
CTCCCAGGCGGCAAGATGGGCTACCTGAAGAGGAACGGGGACGGGAGCCTGCTCTACAGTGTGGTCAACACGGCCGAGCC
AGACGCTGATGAGGAGGAGACCCACCCGGTGGACTTGAGCTCACTCTCCAGTAAGCTACTCCCAGGCTTCACCACGCTGG
GCTTCAAAGACGAGAGAAGAAACAAAGTCACCTTTCTCTCCAGTGCCACTACTGCGCTTTCGATGCAGAATAATTCAGTA
TTTGGCGACTTGAAGTCGGACGAGATGGAGCTGCTCTACTCAGCCTACAGAGATGAGACAGGCATGCAGTGTGCGCTGAG
CCTGCAGGAGTTTGTGAAGGATGCTGGGAGCTACAGCAAGAAAGTGGTGGACGACCTCCTGGACCAGATCACAGGCGGAG
ACCACTCTAGGACGCTCTTCCAGCTGAAGCAGAGAAGAAATGTTCCCATGAAGCCTCCAGATGAAGCCAAGGTTGGGGAC
ACCCTAGGAGACAGCAGCAGCTCTGTTCTGGAGTTCATGTCGATGAAGTCCTATCCCGACGTCTCTGTGGATATCTCCAT
GCTCAGCTCTCTGGGGAAGGTGAAGAAGGAGCTGGACCCTGACGACAGCCATTTGAACTTGGATGAGACGACGAAGCTCC
TGCAAGACCTGCACGCAGCACAGGCGGAGCGCGGTGGATCTCGGCCGTCGTCCAACCTCAGCTCCCTGTCCAACGCCTCC
GAGAGGGACCAGCACCACCTGGGAAGCCCTTCTCGCCTGAGTGTCGGGGAGCAGCCAGACGTCACCCACGACCCCTATGA
GTTTCTTCAGTCTCCAGAGGCTGCGGCCTCTGCCAAGACC

Alignment

ORF - retro_ptro_2061 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.61 %
• Parental protein coverage: 71.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQQAALLGNEETAVEEPVPEVVPVQVETAKKSKKPSREVISCMFEPEGNACSLTDSTTEEHVLALVEHAA
          S.QAALLGNEETAVEEPVPEVVPVQVETAK.SKKPSREVISCMFEPEGNACSLTDSTTEEHVLALVEHAA
Retrocopy SKQAALLGNEETAVEEPVPEVVPVQVETAKTSKKPSREVISCMFEPEGNACSLTDSTTEEHVLALVEHAA

Parental  DEARDRINRFLPGGKMGYLKRNGDGSLLYSVVNTAEPDADEEETHPVDLSSLSSKLLPGFTTLGFKDEKR
          DEARDRINRFLPGGKMGYLKRNGDGSLLYSVVNTAEPDADEEETHPVDLSSLSSKLLPGFTTLGFKDE.R
Retrocopy DEARDRINRFLPGGKMGYLKRNGDGSLLYSVVNTAEPDADEEETHPVDLSSLSSKLLPGFTTLGFKDERR

Parental  NKVTFLSSATTALSMQNNSVFGDLKSDEMELLYSAYRDETGVQCALSLQEFVKDAGSYSKKVVDDLLDQI
          NKVTFLSSATTALSMQNNSVFGDLKSDEMELLYSAYRDETG.QCALSLQEFVKDAGSYSKKVVDDLLDQI
Retrocopy NKVTFLSSATTALSMQNNSVFGDLKSDEMELLYSAYRDETGMQCALSLQEFVKDAGSYSKKVVDDLLDQI

Parental  TGGDHSRTLFQLKQRRNVPMKPPDEAKVGDTLGDSSSSVLEFMSMKSYPDVSVDISMLSSLGKVKKELDP
          TGGDHSRTLFQLKQRRNVPMKPPDEAKVGDTLGDSSSSVLEFMSMKSYPDVSVDISMLSSLGKVKKELDP
Retrocopy TGGDHSRTLFQLKQRRNVPMKPPDEAKVGDTLGDSSSSVLEFMSMKSYPDVSVDISMLSSLGKVKKELDP

Parental  DDSHLNLDETTKLLQDLHEAQAERGGSRPSSNLSSLSNASERDQHHLGSPSRLSVGEQPDVTHDPYEFLQ
          DDSHLNLDETTKLLQDLH.AQAERGGSRPSSNLSSLSNASERDQHHLGSPSRLSVGEQPDVTHDPYEFLQ
Retrocopy DDSHLNLDETTKLLQDLHAAQAERGGSRPSSNLSSLSNASERDQHHLGSPSRLSVGEQPDVTHDPYEFLQ

Parental  SPEAAASAKT
          SPEAAASAKT
Retrocopy SPEAAASAKT

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
SRP007412_brain_prefrontal_cortex	2.52 RPM	14.48 RPM
SRP007412_cerebellum	2.01 RPM	18.57 RPM
SRP007412_heart	0.52 RPM	3.15 RPM
SRP007412_kidney	1.02 RPM	6.90 RPM
SRP007412_liver	0.75 RPM	4.06 RPM
SRP007412_testis	0.42 RPM	7.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2061 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000008103	3 retrocopies	retro_ptro_1840, retro_ptro_2379, retro_ptro_2384,
Pan troglodytes	ENSPTRG00000016688	1 retrocopy	retro_ptro_2061 ,