RetrogeneDB ID: retro_ggor_2435

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:65751153..65752015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUFIP1
• Ensembl ID: ENSGGOG00000000356
• Aliases: None
• Description: None

Sequence

>retro_ggor_2435
GAACCAGTTTTTCACTTTTTTTGTGATACCTGTGATCGTGGTTTTAAAAATCAAGAAAAGTATGACAAACATGTCTGAAC
ATACAAAATGCCCTGAAGTAGATTGCTCTTTTACTGCACACGAGAAGACTGTCCAGTTCCATTGGAGAAATATGCATGCT
CCTGGCATGAAGATCAAGTTAGACACTCCAGAGGAAATTGCACAGTGGAGGGAAGAAAGAAGGAAAAACTAGCCAACTCT
GGCCAATAATGAAAGGAAGAAGAAGTTAAAACTTGAAAAGGAGAAGAGAGGAGCAGTATTGACAACAACACAATATGGCA
AGATGAAGGGGATATCCAGACATTCACAAATGGCAAAGATCAGAAGTCCTGGCGAGAATCACAAATGGAAAAACGACAAT
TCTAGACAGAGAGCAGTCACTGGATCAGGCAATCACTTGTGTGATTTGAAGCCAGAAGGTCCACCTGAGGCAAATGCAGA
TCCTCTTGGTGTTTTGATAAACAGTGATTCTGAGTCTGATAAGGAGGAGAAACCACAGCATTCTGTGATACCCAAGGAAG
TGACACGAACCCTATGCTCACTAATGAGTAGCTATGGCAGTCTTTCAGGGTCAGAGAGTGAGCCAGAAGAAACTCCCATC
AAGACTGAAGCAGATGTTTTGGCAGAAAACCAGGTTCTTGATAGCAGTGCTCCTAAGAGTCCAAGTCAAGATGGTAAAGC
AACTGTTAGAAATTTTTCAGAAGCCAAGAGTGAGAACCGAAAGAAAAGTTTTGAAAAGACAAACCCTAAGAGAAAAAAAG
ATTATCACAACTATCAAACGTTATTCGAACCAAGAACACACCATCCATATCTCTTGGAAATG

Alignment

ORF - retro_ggor_2435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.45 %
• Parental protein coverage: 67.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPVFHFFCDTCDRGFKNQEKYDKHMSEHTKCP-EVDCSFTAHEKIVQFHWRNMHAPGMKKIKLDTPEEIA
          EPVFHFFCDTCDRGFKNQEKYDKH.....K.P.EVDCSFTAHEK.VQFHWRNMHAPGM.KIKLDTPEEIA
Retrocopy EPVFHFFCDTCDRGFKNQEKYDKHV*TY-KMP>EVDCSFTAHEKTVQFHWRNMHAPGM-KIKLDTPEEIA

Parental  RWREERRKNYPTLANIERKKKLKLEKEKRGAVLTTTQYGKMKGMSRHSQMAKIRSPGKNHKRKNDNSRQR
          .WREERRKN.PTLAN.ERKKKLKLEKEKRGAVLTTTQYGKMKG.SRHSQMAKIRSPG.NHK.KNDNSRQR
Retrocopy QWREERRKN*PTLANNERKKKLKLEKEKRGAVLTTTQYGKMKGISRHSQMAKIRSPGENHKWKNDNSRQR

Parental  AVTGSGNHLCDLKLEGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSESE
          AVTGSGNHLCDLK.EGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVT..LCSLMSSYGSLSGSESE
Retrocopy AVTGSGNHLCDLKPEGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTRTLCSLMSSYGSLSGSESE

Parental  PEETPIKTEADVLAENQVLDSSAPKSPSQDVKATVRNFSEAKSENRKKSFEKTNPKRKKDYHNYQTLFEP
          PEETPIKTEADVLAENQVLDSSAPKSPSQD.KATVRNFSEAKSENRKKSFEKTNPKRKKDYHNYQTLFEP
Retrocopy PEETPIKTEADVLAENQVLDSSAPKSPSQDGKATVRNFSEAKSENRKKSFEKTNPKRKKDYHNYQTLFEP

Parental  RTHHPYLLEM
          RTHHPYLLEM
Retrocopy RTHHPYLLEM

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	0.29 RPM	3.02 RPM
SRP007412_cerebellum	0.12 RPM	1.93 RPM
SRP007412_heart	0.03 RPM	0.38 RPM
SRP007412_kidney	0.49 RPM	2.78 RPM
SRP007412_liver	0.40 RPM	1.90 RPM
SRP007412_testis	0.93 RPM	5.39 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_2435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2435 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000083635	1 retrocopy	retro_hsap_3608,
Gorilla gorilla	ENSGGOG00000000356	1 retrocopy	retro_ggor_2435 ,
Pan troglodytes	ENSPTRG00000005838	2 retrocopies	retro_ptro_2439, retro_ptro_2989,