RetrogeneDB ID: retro_ggor_2150

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:10298629..10299064(+)
• Located in intron of: ENSGGOG00000005444

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG12
• Ensembl ID: ENSGGOG00000016888
• Aliases: None
• Description: None

Sequence

>retro_ggor_2150
GTCTCTCCAAGCAAGATGGTGGAGGGGCTGCAGTCCATGTTGCAGCTTCCTCCCTCAAGTGCTACTGGAGGGGAAGGACT
TACGGAGGTCTCCCCAGAAACAACCACCCTGGAGCCCCCGTCTTCCGCTGCAGTTTCTCCGGGAACAGAGGAACCTGCTG
GTGACACCAAGAAAAAAATTGACATTTTGCTAAAGGCTGTGGGGGATACTCCTATTATGAAAACAAAGAAGTGGGCAGTA
GAGTGAACATGAACCATCCAAGGACTCATTGACTTCATCAAAAAGTTTCTTAAACTTGTGGCCTCAGAACAGTTGTTTAT
TTATGTGAATCAGTCCTTTGCTCCTTCCCCAGACCAAGAAGTTGGAACTCTCTATGAGTGTTTTGGCAGTGATGGTAAAC
TGGTTTTACATTACTGCAAGTCTCAGGCATGGGGA

Alignment

ORF - retro_ggor_2150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 77.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFPSKMAEESQSVLQLPPSSAAGGEGLTDVSPETTTPEPPSSAAVSPGTEEPAGDTKKKIDILLKAVGDT
          V.PSKM.E..QS.LQLPPSSA.GGEGLT.VSPETTT.EPPSSAAVSPGTEEPAGDTKKKIDILLKAVGDT
Retrocopy VSPSKMVEGLQSMLQLPPSSATGGEGLTEVSPETTTLEPPSSAAVSPGTEEPAGDTKKKIDILLKAVGDT

Parental  PIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCK
          PIMKTKKWAVE.T.TIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCK
Retrocopy PIMKTKKWAVE*T*TIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCK

Parental  SQAWG
          SQAWG
Retrocopy SQAWG

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	5.61 RPM
SRP007412_cerebellum	0.04 RPM	4.92 RPM
SRP007412_heart	0.00 RPM	1.25 RPM
SRP007412_kidney	0.00 RPM	4.70 RPM
SRP007412_liver	0.08 RPM	5.35 RPM
SRP007412_testis	0.10 RPM	12.64 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_2150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2150 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1860
Pan troglodytes	retro_ptro_1240
Pongo abelii	retro_pabe_1518

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150 ,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518, retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,