RetrogeneDB ID: retro_ptro_162

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:78528964..78530164(+)
• Located in intron of: ENSPTRG00000000884

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC55
• Ensembl ID: ENSPTRG00000008957
• Aliases: NSRP1, CCDC55
• Description: None

Sequence

>retro_ptro_162
AAGAGAGAGCTGAAGAAGAAAGAAAAAAGGGCTGCTGCACTGGAAGCGTGTTTGGATGTAACCAAGCAGAAAGATCTCAG
TGGATTTTATAGACACTTACTAAATCAAGCAGTTGGTGAAGAGGAAGTACCTAAATGCAGCTTTCGTGAAGCCAGATCTG
GTATAAAGGAAGAGAAATCAAGGGGCTACTCTGATGAAGTAAGTTCAAAAAACAGAATACCACAATAGAAATGCATTCTT
CAAACTGATGTGAAAGTAGAGGAAAACCCAGATGCAGACAGTGACTTTGATGCTAAGAGCAGCAAGGATGATGAAATAAA
GAAACTAGAGTGAACTGCAGAAGGGAAAAGGTCATAGAGACCCCTGAGAATCACCCCCAAGCACCACAGGAATCAAAACC
ACTCTCAGTCACCTAGTGAAGAAAGAGGGCACAGTGCCAGACACCACACGAAAGGATCACGAACATCGAGAGGACACGAG
AAAAGGGAAGATCAGCACCAACAGAAGCAATCCAGAGACGAGGAGAACCATTACACTGACCGTGATTACCAGAAAGAAAG
GGATTCTCATAGGCACAGGAGACCAGTCATAGAGATTCCCATTGGAAGAGGCATGAACAGGAAGATAAACTAAGGGCGAG
GGACCAAAGAGAAAGAAGTGACAGAGTGTGGAAAAGGGAGAAAGATGGGGAGAAATATTCCCAAAGAGAACAAGAAAGAG
AGACAACAAAATGATCAGAACCGACACAGTGAGAAAGGAGAGAAGGAAGAGAAAAGCAAAGCAAAGGAAGAGCGTATGAA
AGTAAGGAAAGAAAGATATGAAAATAATGATAAATACAGAGATAGAGAAAAACAAGAAGTAAGTGTTTGATCTTCAGAAA
GAAATCTTCAGAAAGGAAAGCAGCCCAAGTTCTAGGGCAAAGGATAAATTTCTTGACCAAGAAAGATCCAACAAAATGAA
AAACATGACAAAAGACAAAGAAACCAGGAGAAACCCTCTAATTCTGAATCATCACTGGGAGCAAAACACAGACTCACAGA
AAGGCAAGAGAAGGGTAAAGAACAAGAGAGACCACCTGAGGCAGTGAGCAAGTTTGCAAAGAGGAACAACGAAGAAACTG
TAATGTCAGCTAGAGACAGGTACTTGGCCAGGCAGATGGTGCAGGTTAATGCAAAGAGCTATATTGAGAAACAAGATGAT

Alignment

ORF - retro_ptro_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 72.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RAEEEEREKRAAALEACLDVTKQKDLSGFYRHLLNQAVGEEEVPKCSFREARSGIKEEKSRGFSNEVSSK
          ..E....EKRAAALEACLDVTKQKDLSGFYRHLLNQAVGEEEVPKCSFREARSGIKEEKSRG.S.EVSSK
Retrocopy KRELKKKEKRAAALEACLDVTKQKDLSGFYRHLLNQAVGEEEVPKCSFREARSGIKEEKSRGYSDEVSSK

Parental  NRIPQEKCILQTDVKVEENPDADSDFDAKSSADDEI-EETRVNCRREKVIETPEN-DFKHHRSQNYSRSP
          NRIPQ.KCILQTDVKVEENPDADSDFDAKSS.DDEI..ETRVNCRREKVIETPEN...KHHR.QN.S.SP
Retrocopy NRIPQ*KCILQTDVKVEENPDADSDFDAKSSKDDEI<KETRVNCRREKVIETPEN>TPKHHRNQNHSQSP

Parental  SEERGHSTRHHTKGSRTSRGHEKREDQHQQKQSRDQENHYTDRDYRKERDSHRHR-EASHRDSQWKRHEQ
          SEERGHS.RHHTKGSRTSRGHEKREDQHQQKQSRD.ENHYTDRDY.KERDSHRHR.E.SHRDS.WKRHEQ
Retrocopy SEERGHSARHHTKGSRTSRGHEKREDQHQQKQSRDEENHYTDRDYQKERDSHRHR<ETSHRDSHWKRHEQ

Parental  EDKPRARDQRERSDRVWKREKDREKYSQREQERD-RQQNDQNRPSEKGEKEEKSKAKEEHMKGRKERYEN
          EDK.RARDQRERSDRVWKREKD.EKYSQREQER...Q.............E.KSKAKEE.MK.RKERYEN
Retrocopy EDKLRARDQRERSDRVWKREKDGEKYSQREQERE>QQNDQNRHSEKGEKEE-KSKAKEERMKVRKERYEN

Parental  NDKYRDREKREVGVQSSERNRDRKESSP-NSRAKDKFLDQERSNKMRNMAKDKERNQEKP-SNSESSLGA
          NDKYRDREK.EV.V.SSERN...K...P..SRAKDKFLDQERSNKM.NM.KDKE.....P.SNSESSLGA
Retrocopy NDKYRDREKQEVSV*SSERNL-QKGKQP>SSRAKDKFLDQERSNKMKNMTKDKE-TRRNP<SNSESSLGA

Parental  KHRLTEERQEKGKEQERPPEAVSKFAKRNNEETVMSARDRYLARQMARVNAKTYIEKEDD
          KHRLT.ERQEKGKEQERPPEAVSKFAKRNNEETVMSARDRYLARQM..VNAK.YIEK.DD
Retrocopy KHRLT-ERQEKGKEQERPPEAVSKFAKRNNEETVMSARDRYLARQMVQVNAKSYIEKQDD

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	0.46 RPM	17.45 RPM
SRP007412_cerebellum	0.25 RPM	35.71 RPM
SRP007412_heart	0.17 RPM	37.10 RPM
SRP007412_kidney	0.18 RPM	29.71 RPM
SRP007412_liver	0.07 RPM	23.18 RPM
SRP007412_testis	0.53 RPM	89.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_162 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_162 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_457

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009868	1 retrocopy	retro_mdom_391,
Pongo abelii	ENSPPYG00000008130	1 retrocopy	retro_pabe_457,
Pan troglodytes	ENSPTRG00000008957	1 retrocopy	retro_ptro_162 ,
Sarcophilus harrisii	ENSSHAG00000003513	1 retrocopy	retro_shar_342,