RetrogeneDB ID: retro_ggor_1687

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:63533346..63533690(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSGGOG00000000548
• Aliases: None
• Description: None

Sequence

>retro_ggor_1687
ATAAAAGACAAAGAACGGCAACAGAAGAAAAGATAATAAGAAATCAAGAAGAAGTTAGAAGAACGTGAAAAACCTAAAGT
GCTAACACCAGAAAAAATAGCAGATAAATTGCAACTAAAGAAATCACAGAAAAAGTCAGATCTCGAATTAGCAAAATAAA
CCTTTGGTGTTAATAATACAGTTTATGAAATAGATAGTTACGAACCTCTTTAAGAGATAACTTCAGAGTTTGGAAAGTTA
CTAAAGACAAAAATTACACAGTATGAAAAGTAACTATATTACACCAGTTTTTTTAAGCCTCAGTTTGGGATGAGTGTATT
TCATCAGAAATTGATGACTTGCAG

Alignment

ORF - retro_ggor_1687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 52.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IKEKERQQKKRQEEIKKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVYGIDAMNP
          IK.KERQQKKR..EIKK.LEE.E.PKVLTPE...ADKL.LKK.Q..SDLELAK.TFGVNNTVY.ID...P
Retrocopy IKDKERQQKKR**EIKKKLEEREKPKVLTPEK-IADKLQLKKSQKKSDLELAK*TFGVNNTVYEIDSYEP

Parental  -SSRDDFTEFGKLLKD-KITQYEKSLYYASFLE-VLVRDVCISLEIDDLK
          .S.RD.F....K..KD.KITQYEK.LYY.SF.....V.D.CIS.EIDDL.
Retrocopy <SLRDNFRVW-KVTKD>KITQYEK*LYYTSFFK<ASVWDECISSEIDDLQ

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	17.65 RPM
SRP007412_cerebellum	0.00 RPM	12.37 RPM
SRP007412_heart	0.00 RPM	5.38 RPM
SRP007412_kidney	0.00 RPM	19.22 RPM
SRP007412_liver	0.00 RPM	11.05 RPM
SRP007412_testis	0.00 RPM	41.34 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_1687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Echinops telfairi	ENSETEG00000005052	1 retrocopy	retro_etel_1376,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687 , retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,