RetrogeneDB ID: retro_ggor_1814

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:111889670..111890076(-)
• Located in intron of: ENSGGOG00000002675

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_1814
CAGAAGCTGAAGACCATGTCACAGCTACCTCCCTTAACTGCTGCTGGCAGCAAAGGACTTACTCTAGAGGTCTCCCCAAA
ACAGGCACTTCAGACCCCCCTTATTCCACTGTAGTTTCCTGGGACACAGGATCCTGCTGGCAACATCAAGAAAAATCTGA
CATCCTACTAAAGGCTGTGGGACATGTTCCTATTATGCAAACAAAGAAGCAGGCAGTAAAGTGAACTCGAACCATCCAAA
GACTCCTTGACTTCATCAAAAAAGTTCCTTAAACTTGCAACCTCAGTTGTTTATTTATGTGAGTCAGGCTTTTGCTCTTT
CCCTGGACCAGGAATTTGGAACCTTCTATGAGCGTTTCAGCAGTGATGGTAAACTAGTTCTACATTACTGCAAATCTCAG
GCATGG

Alignment

ORF - retro_ggor_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.52 %
• Parental protein coverage: 73.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EESQSVLQLPPSSAAGGEGLT-DVSPETTTPEPPSSAAVSPGTEEPAGDTKK-KIDILLKAVGDTPIMKT
          .......QLPP..AAG..GLT..VSP.......P......PGT..PAG..KK.K.DILLKAVG..PIM.T
Retrocopy QKLKTMSQLPPLTAAGSKGLTLEVSPKQAL-QTPLIPL*FPGTQDPAGNIKK<KSDILLKAVGHVPIMQT

Parental  KKWAVERTRTIQGLIDFI-KKFLKLVASEQLFIYVNQS-FAPSPDQEVGTLYECF-GSDGKLVLHYCKSQ
          KK.AV..TRTIQ.L.DFI.KKFLKL..S.....Y...S.F...P......L...F..SDGKLVLHYCKSQ
Retrocopy KKQAVK*TRTIQRLLDFI>KKFLKLATS---VVYLCESGFCSFPGPGIWNLL*AF>SSDGKLVLHYCKSQ

Parental  AW
          AW
Retrocopy AW

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	0.00 RPM	4.92 RPM
SRP007412_heart	0.00 RPM	1.25 RPM
SRP007412_kidney	0.04 RPM	4.70 RPM
SRP007412_liver	0.03 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_1814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1814 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1748
Pongo abelii	retro_pabe_2158

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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,