RetrogeneDB ID: retro_ggor_2384

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:144208196..144208823(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARL
• Ensembl ID: ENSGGOG00000000416
• Aliases: None
• Description: None

Sequence

>retro_ggor_2384
GGTATCATAGCTGCAAACGTCCTTGTATTCTGTTTGTGGAGAGTACCTTCTCTGCAGTGGACAGTGATCTGATATTTCAA
ATCTAATCTAGCCTCAAAAGTCCGTTGTTCTCCAATGTTGCTGTCAACATTCAATCATTTCTCCTTATTTCACATGGCAG
CAAATATGTATGTTTTGTGGAGCTTCTCCTTCAGTATAGTGAACATTCTGGGTCAAGAGCAGTTCATGGCAGTGTACCTA
TCTGCAGGTGTTATTTCCAATTTTGTCAGTTATGTGTGTAAAGTTGCCACACGAAGATATGGACCATCACTTGGTGCATC
TCGCGCCATCATGATGATCCTCGCAGCTGTCCGCACTAAGATCCGGGAAGGGAGGCTTACCATTATTTACTTCCAATGTT
CACATTCACAGCAGGAAATGCCCTACAATCCATTAACGCCACGGATATGGCAGGAATGATCCTGGGACGGAAATTTTTTG
ATTATGCAGCACATCTTGGGGGAGCTCTCTTTGGAATATGGTATGTTACTTACACTCATGAACTGATTTGGAAGAACAGG
GAGCCTCTAGTGAAAATCTGGCATGAAATGAGGACTAATGCCCCCCCAAAAAAGAGGTGGCTCTAAG

Alignment

ORF - retro_ggor_2384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.31 %
• Parental protein coverage: 55. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIIAANVLVFCLWRVPSLQRTMIRYFTSNPASKVLCSPMLLSTFSHFSLFHMAANMYVLWSFSSSIVNIL
          GIIAANVLVFCLWRVPSLQ.T.I.YF.SN.ASKV.CSPMLLSTF.HFSLFHMAANMYVLWSFS.SIVNIL
Retrocopy GIIAANVLVFCLWRVPSLQWTVI*YFKSNLASKVRCSPMLLSTFNHFSLFHMAANMYVLWSFSFSIVNIL

Parental  GQEQFMAVYLSAGVISNFVSYVGKVATGRYGPSLGASGAIMTVLAAVCTKIPEGRLAIIF-LPMFTFTAG
          GQEQFMAVYLSAGVISNFVSYV.KVAT.RYGPSLGAS.AIM..LAAV.TKI.EGRL.II..LPMFTFTAG
Retrocopy GQEQFMAVYLSAGVISNFVSYVCKVATRRYGPSLGASRAIMMILAAVRTKIREGRLTIIY<LPMFTFTAG

Parental  NALKAIIAMDTAGMILGWKFFDHAAHLGGALFGIWYVTYGHELIWKNREPLVKIWHEIRTNG-PKKGGGS
          NAL..I.A.D.AGMILG.KFFD.AAHLGGALFGIWYVTY.HELIWKNREPLVKIWHE.RTN..P.K.GGS
Retrocopy NALQSINATDMAGMILGRKFFDYAAHLGGALFGIWYVTYTHELIWKNREPLVKIWHEMRTNA>PQKRGGS

Parental  K
          K
Retrocopy K

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	22.97 RPM
SRP007412_cerebellum	0.98 RPM	22.46 RPM
SRP007412_heart	0.03 RPM	12.04 RPM
SRP007412_kidney	0.33 RPM	39.34 RPM
SRP007412_liver	0.90 RPM	20.73 RPM
SRP007412_testis	0.10 RPM	32.63 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_2384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2384 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384 ,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,