RetrogeneDB ID: retro_ptro_1936

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:154286181..154286782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30
• Ensembl ID: ENSPTRG00000016598
• Aliases: None
• Description: None

Sequence

>retro_ptro_1936
GCTTCACGCCTGGGCAGTGGGGAGGCGGCAGCCGCAGTGGCCGCTGTGGTCGCCAGTGCCTCGTCCGGGAAATCGGGGCT
AAGGGGCCGGGCGCAGGGGCGGTCTCAGCGGCTGGGCCCCTGGGGGTGGCCAGGCCGGGCTCCTGGCAACTGTGCAGCCT
GCGGAGGATGGTGAGCGGTGCGGTCGGGCAGCAGGCAACCCAGCTTCAGCAAGAGGATCCAGAAGAGCATATCCCAGAAG
GTGAAGATCGAGCTGGATAAGAGCGCAGGCATCTTTACATATGTGATTATCATAAAAACTTAATTCAGAGTATTCGAAAC
AGAAGAGAAAAGGGAGTGATGATGATGGAGGTGATTCCCCTGTTCAAGATTTCGATACCCCAGAGGTTGATTTATACCAA
TTACAAGTAAATACACTTAGGAGATACAAAAGACACTTAAAGCCACCAACCAGACCAGGACTTAAAGCACAACTTGTTGA
GATAGTTGGTTGCCACTTTAGGTCTATTCCAGTGAGTGAAAAAGACACCTTAACATATTTCATCTAATCAGTGAAGAATG
ACAAGAACAAATCAGATCTCAAGGTTGATAGTGGTGTTCAC

Alignment

ORF - retro_ptro_1936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 93.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AAAVAAVVAAAAAAASAGNGTGAGTG-AEVPGAGAVSASGPPGAAGPGPGQLCCLR-EDGERCGRAAGNA
          A.......AAAA.AA..........G.A..PGAGAVSA.GP.G.A.PG..QLC.LR.EDGERCGRAAGN.
Retrocopy ASRLGSGEAAAAVAAVVASASSGKSG<AKGPGAGAVSAAGPLGVARPGSWQLCSLR<EDGERCGRAAGNP

Parental  -SFSKRIQKSISQKKVKIELDKSA-RHLYICDYHKNLIQSVRNRRKRKG-SDDDGGDSPVQDIDTPEVDL
          .SFSKRIQKSISQK.VKIELDKSA.RHLYICDYHKNLIQS.RNRR..KG.SDDDGGDSPVQD.DTPEVDL
Retrocopy <SFSKRIQKSISQK-VKIELDKSA<RHLYICDYHKNLIQSIRNRRE-KG<SDDDGGDSPVQDFDTPEVDL

Parental  YQLQVNTLRRYKRHFKLPTRPGLNKAQLVEIVGCHFRSIPVNEKDTLTYFIYSVKNDKNKSDLKVDSGVH
          YQLQVNTLRRYKRH.K.PTRPGL.KAQLVEIVGCHFRSIPV.EKDTLTYFI.SVKNDKNKSDLKVDSGVH
Retrocopy YQLQVNTLRRYKRHLKPPTRPGL-KAQLVEIVGCHFRSIPVSEKDTLTYFI*SVKNDKNKSDLKVDSGVH

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	0.04 RPM	4.72 RPM
SRP007412_cerebellum	0.11 RPM	5.41 RPM
SRP007412_heart	0.03 RPM	2.54 RPM
SRP007412_kidney	0.03 RPM	2.07 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.00 RPM	24.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1936 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1936 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2864
Gorilla gorilla	retro_ggor_1980
Macaca mulatta	retro_mmul_1467

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164105	1 retrocopy	retro_hsap_2864,
Gorilla gorilla	ENSGGOG00000005082	2 retrocopies	retro_ggor_1980, retro_ggor_3072,
Macaca mulatta	ENSMMUG00000002401	1 retrocopy	retro_mmul_1467,
Monodelphis domestica	ENSMODG00000003536	1 retrocopy	retro_mdom_608,
Nomascus leucogenys	ENSNLEG00000006666	1 retrocopy	retro_nleu_605,
Pongo abelii	ENSPPYG00000015205	1 retrocopy	retro_pabe_2366,
Pan troglodytes	ENSPTRG00000016598	1 retrocopy	retro_ptro_1936 ,