RetrogeneDB ID: retro_ptro_2439

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:66349643..66350609(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUFIP1
• Ensembl ID: ENSPTRG00000005838
• Aliases: None
• Description: None

Sequence

>retro_ptro_2439
CCCCTTGATTCTCAGCCTCAACCCAGCGGCCAGCCTTGGAGTTTCCATGCTTCCACATCGTGGAATTGGAGACAGTCTTC
TGATAGGTTTCCTCGGCATCAGAAGTCCTTCAACCCTTCAGTTAAAAATTCTTATTATCCACGAAAGTATGATGCAAAAT
TCACAGACTTCAGCTTACCTCCCAGTAGAAAACAGAAAAAAAAGAAAAGAAAGGAACCAGTTTTTCACTTTTTTTGTGAT
ACCTGTGATCGTGGTTTTAAAAATCAAGAAAAGTATGACAAACACGTCTGCACATACAAAATGCCCTGAAGTAGATTGCT
CTTTTACTGCACACGAGAAGACTGTCCAGTTCCATTGGAGAAATATGCATGCTCCTGGCATGAAGATCAAGTTAGACACT
CCAGAGGAAATTGCACAGTGGAGGGAAGAAAGAAGGAAAAACTAGCCAACTCTGGCCAATATTGAAAGGAAGAAGAAGTT
AAAACTTGAAAAGGAGAGAGGAGCAGTATTGACAACAACACAATATGGCAAGATGAAGGGGATTTCCAGACATTCACAAA
TGGCAAAGATCAGAAGTCCTGGGAGAATCACAAATGGAAAAACGACAATTCTAGACAGAGAGCAGTCACTGGATCAGGCA
ATCACTTGTGTGATTTGAAGCCAGAAGGTCCACCTGAAGCAAATGCAGATCCTCTTGGTGTTTTGATAAACAGTGATTCT
GAGTCTGATAAGGAGGAGAAACCACAACATTCTGTGATACCCAAGGAAGTGACACCAGCCCTATGCTCACTAATGAGTAG
CTATGGCAGTCTTTCAGGGTCAGAGAGTGAGCCAGAAGAAACTCCCATCAAGACTGAAGCAGACGTTTTGGCAGAAAACC
AGGTTCTTGATAGCAGTGCTCCTAAGAGTCCAAGTCAAGATGTTAAAGCAACTGTCAGAAATTTTTCAGAAGCCAAGAGT
GAGAAC

Alignment

ORF - retro_ptro_2439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLDSQPQPSGQPWNFHASTSWYWRQSSDRFPRHQKSFNPAVKNSYYPRKYDAKFTDFSLPPSRKQKKKKR
          PLDSQPQPSGQPW.FHASTSW.WRQSSDRFPRHQKSFNP.VKNSYYPRKYDAKFTDFSLPPS........
Retrocopy PLDSQPQPSGQPWSFHASTSWNWRQSSDRFPRHQKSFNPSVKNSYYPRKYDAKFTDFSLPPSXXXXXXXX

Parental  KEPVFHFFCDTCDRGFKNQEKYDKHMSEHTKCP-EVDCSFTAHEKIVQFHWRNMHAPGMKKIKLDTPEEI
          .EPVFHFFCDTCDRGFKNQEKYDKH.....K.P.EVDCSFTAHEK.VQFHWRNMHAPGM.KIKLDTPEEI
Retrocopy XEPVFHFFCDTCDRGFKNQEKYDKHVCTY-KMP>EVDCSFTAHEKTVQFHWRNMHAPGM-KIKLDTPEEI

Parental  ARWREERRKNYPTLANIERKKKLKLEKEKRGAVLTTTQYGKMKGMSRHSQMAKIRSPGK-NHKWKNDNSR
          A.WREERRKN.PTLANIERKKKLKLEKE.RGAVLTTTQYGKMKG.SRHSQMAKIRSPG..NHKWKNDNSR
Retrocopy AQWREERRKN*PTLANIERKKKLKLEKE-RGAVLTTTQYGKMKGISRHSQMAKIRSPGR<NHKWKNDNSR

Parental  QRAVTGSGNHLCDLKLEGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSE
          QRAVTGSGNHLCDLK.EGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSE
Retrocopy QRAVTGSGNHLCDLKPEGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSE

Parental  SEPEETPIKTEADVLAENQVLDSNAPKSPSQDVKATVRNFSEAKSEN
          SEPEETPIKTEADVLAENQVLDS.APKSPSQDVKATVRNFSEAKSEN
Retrocopy SEPEETPIKTEADVLAENQVLDSSAPKSPSQDVKATVRNFSEAKSEN

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	5.20 RPM
SRP007412_cerebellum	0.00 RPM	4.02 RPM
SRP007412_heart	0.00 RPM	2.22 RPM
SRP007412_kidney	0.00 RPM	4.71 RPM
SRP007412_liver	0.03 RPM	4.16 RPM
SRP007412_testis	0.11 RPM	15.60 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2439 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2439 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3608
Pan troglodytes	retro_ptro_2989

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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,