RetrogeneDB ID: retro_ggor_1980

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:151091867..151092452(-)
• Located in intron of: ENSGGOG00000028291

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30
• Ensembl ID: ENSGGOG00000005082
• Aliases: None
• Description: None

Sequence

>retro_ggor_1980
GCGGCAGCCGCAGTGGCCGCTGTGGTCGCCAGTGCCTCGTCCGGGAAATTGGGGCTGAGGGGCCGGGCGCAGGGGCGGTC
TCAGCGGCTGGGCCCCTGGGGGCGGCCAGGCCGGGCTCCTGGCAACTGTGCTGCCTGCGGAGGATGGTGAGCGGTGCGGT
CGGGCAGCAGGCAACGCCAGCTTCAGCAAGAGGATCCAGAAGAGCATATCCCAGAAGGTGAAGATCGAGCTGGATAAGAG
CGCAGGCATCTTTACATATGTGATTATCATAAAAACTTAATTCAGAGTATTCGAAACAGAAGAAAGAGAAAAGGGAGTGA
TGATGATGGAGGTGATTCACCTGTTCAAGATTTTGATACCCCAGAGGTTGATTTATACCAATTACAAGTAAATACACTTA
GGAGATACAAAAGACACCTAAAGCCACCAACCAGACCAGGACTTAATAAAGCACAACTTGTTGAGATAGTTGGTTGCCAC
TTTAGGTCTATTCCAGTGAGTGAAAAAGACACCTTAACATATTTCATCTAATCAGTGAAGAATGACAAGAACAAATCAGA
TCTCAAGGTTGATAGTGGTGTTCAC

Alignment

ORF - retro_ggor_1980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.0 %
• Parental protein coverage: 89.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAAAAAASAGNGTGAGTG-AEVPGAGAVSAAGPPGAAGPGPGQLCCLR-EDGERCGRAAGNASFSKRIQK
          AAAA.AA..........G.AE.PGAGAVSAAGP.GAA.PG..QLCCLR.EDGERCGRAAGNASFSKRIQK
Retrocopy AAAAVAAVVASASSGKLG<AEGPGAGAVSAAGPLGAARPGSWQLCCLR<EDGERCGRAAGNASFSKRIQK

Parental  SISQKKVKIELDKSA-RHLYICDYHKNLIQSVRNRRKRKGSDDDGGDSPVQDIDTPEVDLYQLQVNTLRR
          SISQK.VKIELDKSA.RHLYICDYHKNLIQS.RNRRKRKGSDDDGGDSPVQD.DTPEVDLYQLQVNTLRR
Retrocopy SISQK-VKIELDKSA<RHLYICDYHKNLIQSIRNRRKRKGSDDDGGDSPVQDFDTPEVDLYQLQVNTLRR

Parental  YKRHFKLPTRPGLNKAQLVEIVGCHFRSIPVNEKDTLTYFIYSVKNDKNKSDLKVDSGVH
          YKRH.K.PTRPGLNKAQLVEIVGCHFRSIPV.EKDTLTYFI.SVKNDKNKSDLKVDSGVH
Retrocopy YKRHLKPPTRPGLNKAQLVEIVGCHFRSIPVSEKDTLTYFI*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	0.00 RPM	5.90 RPM
SRP007412_cerebellum	0.00 RPM	4.29 RPM
SRP007412_heart	0.03 RPM	1.22 RPM
SRP007412_kidney	0.00 RPM	1.14 RPM
SRP007412_liver	0.00 RPM	1.29 RPM
SRP007412_testis	0.00 RPM	18.13 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1980 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2864
Pan troglodytes	retro_ptro_1936
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,