RetrogeneDB ID: retro_ggor_900

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:107775850..107776401(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000007475
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APOBEC3B
• Ensembl ID: ENSGGOG00000006721
• Aliases: None
• Description: None

Sequence

>retro_ggor_900
GACACATTCACTTACAATTTTACCAATGATCCTTCAGTCTCTGGGCAGCACCAGACCTACCTGTGCTACAAGGTGGAGTG
CCAAAACAATGACGCCTGGGTCCCTCTGGACCAGCACAAGGGCATCCTACCCAGCCAGGCTTTGAATAATCTCAGTTGCT
ATTAAGATTTCCATGTAGAGCAGTGCTTCCTGTACCTGATTTCCTTTTGGAAGCTGGACCGGGCTCAGTGCTACAGGGTC
ACCTGGTTCATCTCCTGGAGTCCCTGCTTCAGCTGTGCCCAGCAAGTGGCTACATTTCATTGGGAGAACAGATGTGTGAG
CCTGCACATCTTCGCTGCATGCATCTATAATTATCTCCCAGGATATGAGGGGCCGTGCATGCTGCAGAGGGCTGGGACCC
AAATCTCCATCATGACCTCCAGAAGTTTAGGCACTGCTGGGTCACCTTTGTGGACCACCAGGGACGTCCCTTCCAGCCCT
GGGATGGACTAGATGAGCACAGTCAAGCCCTAAGTGGGAGGCTGCAGGCCATTCTCCAGAATCAGGAAAAC

Alignment

ORF - retro_ggor_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.64 %
• Parental protein coverage: 92.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTFTSNFNNDLLVLRRHQTYLCYEVERLDNGTWVKMDQHRGFLHNQAKNLLCGFYGRHAELRFLDLVPSL
          DTFT.NF.ND..V...HQTYLCY.VE...N..WV..DQH.G.L..QA.N.L......H.E..FL.L....
Retrocopy DTFTYNFTNDPSVSGQHQTYLCYKVECQNNDAWVPLDQHKGILPSQALNNLSCY*DFHVEQCFLYLISFW

Parental  QLDPAQIYRVTWFISWSPCFSWGCAGQVCEFLQENTHMRLRIFAARIYDYDPLYKKALQMLRDAGAQVSI
          .LD.AQ.YRVTWFISWSPCFS..CA.QV..F..EN....L.IFAA.IY.Y.P.Y.....ML..AG.Q.SI
Retrocopy KLDRAQCYRVTWFISWSPCFS--CAQQVATFHWENRCVSLHIFAACIYNYLPGYEGPC-MLQRAGTQISI

Parental  MT-YDEFKHCWDTFVYRQGCPFQPWDGLEEHSQALSGRLQAILQNQGN
          MT....F.HCW.TFV..QG.PFQPWDGL.EHSQALSGRLQAILQNQ.N
Retrocopy MT<LQKFRHCWVTFVDHQGRPFQPWDGLDEHSQALSGRLQAILQNQEN

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	0.10 RPM	0.38 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.69 RPM
SRP007412_kidney	0.12 RPM	0.98 RPM
SRP007412_liver	0.08 RPM	1.16 RPM
SRP007412_testis	0.10 RPM	1.04 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_900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_900 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_959

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000006721	1 retrocopy	retro_ggor_900 ,
Pongo abelii	ENSPPYG00000011831	1 retrocopy	retro_pabe_959,