RetrogeneDB ID: retro_ggor_1960

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:99621712..99622133(-)
• Located in intron of: ENSGGOG00000010890

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMFG
• Ensembl ID: ENSGGOG00000006957
• Aliases: None
• Description: None

Sequence

>retro_ggor_1960
ATGAGTGAGTCTTTGGTGGTTTTGATGTTGCTGAAGATTTAGTGGAAAAGCTGAGAAAGTTTCGTTTTCACAAAGAAACG
AACAATGCTTCTATTGTAATGAAGATTGAAGGATAAACGCCTGGTGGTACTGGATGAGGAGCTTGAGGGTATTTCACCCG
ATGAACTTAAAGATGAACTACCTGAACGACAACCTCGTTTCATTGTGTATAGTTATAAATATCAACATAACGGATGGGAG
AGTTCCATATCCTCCGTGCTTTATTTTCTCCAGTCCTGTTGGATGTAAGCCTGAACAACAAATGATATATGCTGGCAGTA
AGAATAAGCTAGTCCAGACAGCTGAACTAACCAAGGTATTTGAAATAAGAAATACGGAAGAACTGACTGAAGAATGGTTA
TGTGAGAAACTTGGATTTTTC

Alignment

ORF - retro_ggor_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.53 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDSLVVC-EVDPELTEKLRKFRFRKETDNAAIIMKVD-KDRQMVVLEEEFQNISPEELKMELPERQPRF
          MS.SLVV...V...L.EKLRKFRF.KET.NA.I.MK.....R..V..E.E...ISP.ELK.ELPERQPRF
Retrocopy MSESLVVL<DVAEDLVEKLRKFRFHKETNNASIVMKIE>DKRLVVLDE-ELEGISPDELKDELPERQPRF

Parental  VVYSYKYVHD-DGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAELTKVFEIRTTDDLTEAWLQEK
          .VYSYKY.H..DGRV.YP.CFIFSSPVGCKPEQQM.YAGSKN.LVQTAELTKVFEIR.T..LTE.WL.EK
Retrocopy IVYSYKYQHN>DGRVPYPPCFIFSSPVGCKPEQQMIYAGSKNKLVQTAELTKVFEIRNTEELTEEWLCEK

Parental  LSFF
          L.FF
Retrocopy LGFF

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	0.05 RPM	7.62 RPM
SRP007412_cerebellum	0.00 RPM	2.05 RPM
SRP007412_heart	0.00 RPM	4.72 RPM
SRP007412_kidney	0.00 RPM	18.52 RPM
SRP007412_liver	0.05 RPM	33.16 RPM
SRP007412_testis	0.00 RPM	6.01 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_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1960 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2818
Pongo abelii	retro_pabe_2209
Macaca mulatta	retro_mmul_1498

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006529	2 retrocopies	retro_dnov_1062, retro_dnov_1435,
Echinops telfairi	ENSETEG00000008573	1 retrocopy	retro_etel_1630,
Gorilla gorilla	ENSGGOG00000006957	1 retrocopy	retro_ggor_1960 ,
Mus musculus	ENSMUSG00000060791	1 retrocopy	retro_mmus_2800,
Ochotona princeps	ENSOPRG00000015157	2 retrocopies	retro_opri_1160, retro_opri_160,
Sarcophilus harrisii	ENSSHAG00000008772	1 retrocopy	retro_shar_803,