RetrogeneDB ID: retro_ptro_3147

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:103689266..103689815(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039683
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CMTM6
• Ensembl ID: ENSPTRG00000014720
• Aliases: None
• Description: Pan troglodytes CKLF-like MARVEL transmembrane domain containing 6 (CMTM6), mRNA. [Source:RefSeq mRNA;Acc:NM_001246505]

Sequence

>retro_ptro_3147
ATGGAGAACGGAGCGGTGTACAGCCCCACTACGGAGGAGGACCCGGGCCCCGCCAGAGGCCCCCGGAGCGGCCTCGCTGC
CTACTTTTTCATGGGCCGGCTCCCATTGCTCCGGCGCGTTCTCAAGGGCTTGCAGCTGTTGCTGTCTCTGCTGGCCTTCA
TCTGTGAAGAAGTTGTATCACAATGTACTTTATGTGGAGGACTTTATTTTTTTGAGTTTGTAAGCTGCAGTGCCTTTCTT
CTGAGTCTCCTTATACTGATTGTGTATTGCACTCCATTTTATGAGAGAGTTGATAACACAAAAGTAAAATCATCGGATTT
TTATATTACTTTGGGAACAGGATGTGTGTTTTTGTTGGCATCCATCATTTTTGTTTCCACACATGACAGGACTTCAGCTG
AGATTGCTGCAATTGTGTTTGGATTTATAGCAAGTTTTATGTTCCTACTTGACTTTGTCACTATGCTGTATGAAAAACGA
CAGGAGTCCCAGCTGAGAAAACCTGAAAATACCACTAGGGCTGAAGCCCTCACTGAGCCACTTAATGCC

Alignment

ORF - retro_ptro_3147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENGAVYSPTTEEDPGPARGPRSGLAAYFFMGRLPLLRRVLKGLQLLLSLLAFICEEVVSQCTLCGGLYF
          MENGAVYSPTTEEDPGPARGPRSGLAAYFFMGRLPLLRRVLKGLQLLLSLLAFICEEVVSQCTLCGGLYF
Retrocopy MENGAVYSPTTEEDPGPARGPRSGLAAYFFMGRLPLLRRVLKGLQLLLSLLAFICEEVVSQCTLCGGLYF

Parental  FEFVSCSAFLLSLLILIVYCTPFYERVDTTKVKSSDFYITLGTGCVFLLASIIFVSTHDRTSAEIAAIVF
          FEFVSCSAFLLSLLILIVYCTPFYERVD.TKVKSSDFYITLGTGCVFLLASIIFVSTHDRTSAEIAAIVF
Retrocopy FEFVSCSAFLLSLLILIVYCTPFYERVDNTKVKSSDFYITLGTGCVFLLASIIFVSTHDRTSAEIAAIVF

Parental  GFIASFMFLLDFVTMLYEKRQESQLRKSENTTRAEALTEPLNA
          GFIASFMFLLDFVTMLYEKRQESQLRK.ENTTRAEALTEPLNA
Retrocopy GFIASFMFLLDFVTMLYEKRQESQLRKPENTTRAEALTEPLNA

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	0.02 RPM	3.83 RPM
SRP007412_cerebellum	0.00 RPM	3.41 RPM
SRP007412_heart	0.00 RPM	6.53 RPM
SRP007412_kidney	0.05 RPM	20.53 RPM
SRP007412_liver	0.03 RPM	20.36 RPM
SRP007412_testis	0.00 RPM	16.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3147 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3147 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015014	1 retrocopy	retro_dnov_1,
Otolemur garnettii	ENSOGAG00000026982	1 retrocopy	retro_ogar_97,
Pan troglodytes	ENSPTRG00000014720	1 retrocopy	retro_ptro_3147 ,
Tursiops truncatus	ENSTTRG00000003526	1 retrocopy	retro_ttru_1857,
Vicugna pacos	ENSVPAG00000003039	1 retrocopy	retro_vpac_376,