RetrogeneDB ID: retro_ptro_2989

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390393.1:32353..33326(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039827
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ptro_2989
CCCCTTGATTCTCAGCCTCAACCCAGCGGCCAGCCTTGGAATTTCCATGCTTCCACATCGTGGTATTGGAGACAGTCTTC
TGATAGGTTTCCTCGGCATCAGAAGTCCTTCAACCCTTCAGTTAAAAATTCTTATTATCCACGAAAGTATGATGAAAAAT
TCACAGACTTCAGCTTACCTCCCAGTAGAAAACAGAAAAAAAAGAAAAGAAAGGAACCAGTTTTTCACTTTTTTTGTGAT
ACCTGTGATCGTGGTTTTAAAAATCAAGAAAAGTATGACAAACACGTCTGAACATACAAAATGCCCTGAAGTAGATTGCT
CTTTTACTGCACACGAGAAGACTGTCCACTTCCATTGGAGAAATATGCATGCTCCTGGCATGAAGAAGATCAAGTTAGAC
ACTCCAGAGGAAATTGCACAGTGGAGGGAAGAAAGAAGGAAAAACTAGCCAACTCTGGCCAATATTGAAAGGAAGAAGAA
GTTAAAACTTGAAAAGGAGAAGAGAGGAGCAGTATTGACAACAACACAATATGGCAAGATGAAGGGGATGTCCAGACATT
CACAAATGGCAAAGATCAGAAGTCCTGGCGAGAATCACAAATGGAAAAACGACAATTCTAGACAGAGAGCAGTCACTGGA
TCAGGCAATCACTTGTGTGATTTGAAGCCAGAAGGTCCACCTGAGGCGAATGCAGATCCTCTTGGTGTTTTGATAAACAG
TGATTCTGAGTCTGATAAGGAGGAGAAACCACAACATTCTGTGATACCCAAGGAAGTGACACCAGCCCTATGCTCACTAA
TGAGTAGCTATGGCAGTCTTTCAGGGTCAGAGAGTGAGCCAGAAGAAACTCCCATCAAGACTGAAGCAGACGTTTTGGCA
GAAAACCAGGTTCTTGATAGCAGTGCTCCTAAGAGTCCAAGTCAAGATGTTAAAGAAACTGTTAGAAATTTTTCAGAAGC
CAAGAGTGAGAAC

Alignment

ORF - retro_ptro_2989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLDSQPQPSGQPWNFHASTSWYWRQSSDRFPRHQKSFNPAVKNSYYPRKYDAKFTDFSLPPSRKQKKKKR
          PLDSQPQPSGQPWNFHASTSWYWRQSSDRFPRHQKSFNP.VKNSYYPRKYD.KFTDFSLPPS........
Retrocopy PLDSQPQPSGQPWNFHASTSWYWRQSSDRFPRHQKSFNPSVKNSYYPRKYDEKFTDFSLPPSXXXXXXXX

Parental  KEPVFHFFCDTCDRGFKNQEKYDKHMSEHTKCP-EVDCSFTAHEKIVQFHWRNMHAPGMKKIKLDTPEEI
          .EPVFHFFCDTCDRGFKNQEKYDKH.....K.P.EVDCSFTAHEK.V.FHWRNMHAPGMKKIKLDTPEEI
Retrocopy XEPVFHFFCDTCDRGFKNQEKYDKHV*TY-KMP>EVDCSFTAHEKTVHFHWRNMHAPGMKKIKLDTPEEI

Parental  ARWREERRKNYPTLANIERKKKLKLEKEKRGAVLTTTQYGKMKGMSRHSQMAKIRSPGKNHKWKNDNSRQ
          A.WREERRKN.PTLANIERKKKLKLEKEKRGAVLTTTQYGKMKGMSRHSQMAKIRSPG.NHKWKNDNSRQ
Retrocopy AQWREERRKN*PTLANIERKKKLKLEKEKRGAVLTTTQYGKMKGMSRHSQMAKIRSPGENHKWKNDNSRQ

Parental  RAVTGSGNHLCDLKLEGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSES
          RAVTGSGNHLCDLK.EGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSES
Retrocopy RAVTGSGNHLCDLKPEGPPEANADPLGVLINSDSESDKEEKPQHSVIPKEVTPALCSLMSSYGSLSGSES

Parental  EPEETPIKTEADVLAENQVLDSNAPKSPSQDVKATVRNFSEAKSEN
          EPEETPIKTEADVLAENQVLDS.APKSPSQDVK.TVRNFSEAKSEN
Retrocopy EPEETPIKTEADVLAENQVLDSSAPKSPSQDVKETVRNFSEAKSEN

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	0.04 RPM	4.02 RPM
SRP007412_heart	0.00 RPM	2.22 RPM
SRP007412_kidney	0.00 RPM	4.71 RPM
SRP007412_liver	0.00 RPM	4.16 RPM
SRP007412_testis	0.21 RPM	15.60 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2989 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2989 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3608
Pan troglodytes	retro_ptro_2439

---

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 ,