RetrogeneDB ID: retro_ggor_1492

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:53888142..53888607(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022308
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFAF1
• Ensembl ID: ENSGGOG00000025980
• Aliases: None
• Description: Complex I intermediate-associated protein 30, mitochondrial [Source:UniProtKB/TrEMBL;Acc:G3RN35]

Sequence

>retro_ggor_1492
CAGTTCTGGGGGAAAGAAGACTTGGATAAGTAGATAGTGACTTCCGAAAAGATGATTGGAGGCAGAAGTGAAGTATTTTT
GAAAATGGGCAAGAATAACCAAAGTGCACTGCTATATGGAACTCTGAGCTCTGAGGTGCCTCAGGATGGGGAGACTACCT
GAAGTGGGTACTGTGCAGTGATATCCAGGATTCCAGGGGGTGCTTTTGAGAGGAAGATGTCTTATGATTGGTCCCAGTTC
AGTACTCTGTATCTCCATGTATGTGGGGATGGTTGGCCTTGGATGATGAATATCAGGGAGGACACAGATATAATCCAGAG
GAAAAACAGATGTATAGTTACTTAATGTTCACCCGTGGGGACTCCTACTGGCAGGAGGTCAAGATCCCTTTTTCCAAATT
TTTTTTTCCCTAATCAAGGAAGAGTACAGGATGTTCAGAGTCAGCTTCTGCTTGACAAGATCTCT

Alignment

ORF - retro_ggor_1492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 55.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QFRGKEDLDKWTVTSDKTIGGRSEVFLKMGKNNQSALLYGTLSSEAPQDGESTRSGYCAMKSRIPRGAFE
          QF.GKEDLDK..VTS.K.IGGRSEVFLKMGKNNQSALLYGTLSSE.PQDGE.T.SGYCA..SRIP.GAFE
Retrocopy QFWGKEDLDK*IVTSEKMIGGRSEVFLKMGKNNQSALLYGTLSSEVPQDGETT*SGYCAVISRIPGGAFE

Parental  RKMSYDWSQFNTLYLRVRGDGRPWMVNIKEDTDFFQRTN-QMYSYFMFTRGGPYWQEVKIPFSK-FFFSN
          RKMSYDWSQF.TLYL.V.GDG.PWM.NI.EDTD..QR.N.QMYSY.MFTRG..YWQEVKIPFSK.....N
Retrocopy RKMSYDWSQFSTLYLHVCGDGWPWMMNIREDTDIIQRKN<QMYSYLMFTRGDSYWQEVKIPFSK>XXXPN

Parental  RGRIRDVQHELPLDKVT
          .GR..DVQ..L.LDK..
Retrocopy QGRVQDVQSQLLLDKIS

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	0.82 RPM	27.19 RPM
SRP007412_cerebellum	0.55 RPM	14.46 RPM
SRP007412_heart	0.56 RPM	16.98 RPM
SRP007412_kidney	0.90 RPM	30.75 RPM
SRP007412_liver	0.74 RPM	17.99 RPM
SRP007412_testis	1.04 RPM	43.30 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_1492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1492 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1683

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000025980	1 retrocopy	retro_ggor_1492 ,
Microcebus murinus	ENSMICG00000016845	1 retrocopy	retro_mmur_637,
Nomascus leucogenys	ENSNLEG00000003587	1 retrocopy	retro_nleu_2733,
Pongo abelii	ENSPPYG00000006373	2 retrocopies	retro_pabe_1683, retro_pabe_1684,
Pan troglodytes	ENSPTRG00000006945	1 retrocopy	retro_ptro_1383,