RetrogeneDB ID: retro_ptro_2015

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:130307837..130308107(+)
• Located in intron of: ENSPTRG00000016433

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9H9ORF80
• Ensembl ID: ENSPTRG00000023472
• Aliases: C9H9orf80, C9orf80
• Description: Pan troglodytes SOSS complex subunit C-like (C9H9orf80), mRNA. [Source:RefSeq mRNA;Acc:NM_001242593]

Sequence

>retro_ptro_2015
CAAGTTGCAATCTTGGCAGAACTGGACAAAGAGAAAAGAAGACTACTTATGCAGAACCAGTCTTCAACAAATCATCCTGG
AGCTAGCATTGCACTCTCGAGACCCTGTCTTAATAAGGACTTCTGGGATCACGCTGAGCCGCAGTATATTGCAGCCCAGC
AGAAGGCAGCTTTGCAGCATGCTCATGCACATTCATTTGGATACTTCATAACTCAAGACTCTGCATTTGGGAACCTGATT
CTTCCTGTTTTACCTCACCTTGACCCAGAA

Alignment

ORF - retro_ptro_2015 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 86.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVAILAELDKEKRKLLMQNQSSTNHPGASIALSRPSLNKDFRDHAEQQHIAAQQKAALQHAHAHSSGYFI
          .VAILAELDKEKR.LLMQNQSSTNHPGASIALSRP.LNKDF.DHAE.Q.IAAQQKAALQHAHAHS.GYFI
Retrocopy QVAILAELDKEKRRLLMQNQSSTNHPGASIALSRPCLNKDFWDHAEPQYIAAQQKAALQHAHAHSFGYFI

Parental  TQDSAFGNLILPVLPRLDPE
          TQDSAFGNLILPVLP.LDPE
Retrocopy TQDSAFGNLILPVLPHLDPE

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	0.14 RPM	9.03 RPM
SRP007412_cerebellum	0.82 RPM	10.43 RPM
SRP007412_heart	0.09 RPM	5.36 RPM
SRP007412_kidney	0.10 RPM	10.09 RPM
SRP007412_liver	0.00 RPM	5.34 RPM
SRP007412_testis	0.21 RPM	4.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2015 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2015 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2980

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006841	1 retrocopy	retro_amel_1661,
Equus caballus	ENSECAG00000008524	1 retrocopy	retro_ecab_187,
Homo sapiens	ENSG00000148153	1 retrocopy	retro_hsap_2980,
Microcebus murinus	ENSMICG00000001130	1 retrocopy	retro_mmur_92,
Nomascus leucogenys	ENSNLEG00000016554	1 retrocopy	retro_nleu_1508,
Oryctolagus cuniculus	ENSOCUG00000016717	1 retrocopy	retro_ocun_335,
Oryzias latipes	ENSORLG00000011577	1 retrocopy	retro_olat_8,
Pan troglodytes	ENSPTRG00000023472	1 retrocopy	retro_ptro_2015 ,
Sorex araneus	ENSSARG00000003661	1 retrocopy	retro_sara_104,
Xiphophorus maculatus	ENSXMAG00000002259	1 retrocopy	retro_xmac_8,