RetrogeneDB ID: retro_ptro_2019

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:141268184..141269417(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOB1
• Ensembl ID: ENSPTRG00000008285
• Aliases: None
• Description: None

Sequence

>retro_ptro_2019
ATGGCTCCAGTGTAGCACGTTGTGGGGGATGCTGGGGCTTTCCTGCGGGATGCGGCTCTGCAGGACATCGGGAAGAACAT
TTACACCATCCGGGAGGTGGTCACTGAGATTCGGGACAAGGCCACATGCAGGCGGCTTGCTGTCCTGCCCTATGAGCTGC
GGTTCAAGGAGCCCTCACTGGAATACGTGCGGCTGGTGACTGAGTTTTCAAAGAAAACAGGAGACTACCCCAGCCTCTCT
GCCACGGACATCCAAGTGCTTGCACTCACATACCAGTTGGAAGCAGAGTTTGTTGGGGTGTCTCACCTAAAACAAGAACC
ACAGAAGGTTAAAGTGAGCTTATCGATTCAGCACCCAGAAACACCTCTGCACATTTCTGGTTTCCATCTGCCCTCCAAGC
CTAAACCCCCACAAGAAACAGAAAAAGGACACCCAGCTTGTGAGCCTGAGAACCTGGAATTTAGTTCCTTCATGTTCTGG
AGAAACCCTCTGCCCAACATCGATCATGAACTGCAGGAGCCGCTGATTGACAGAGGTGAGGACGTTCCAAGTGAGGAGGA
GGAGAAAGAGAACGGGTCTGAAGACAGAAAAGATGACAGCGATGACGACGGGGGTGGCTGGATAACCCCCAGTAACATCA
AGCAGATCCAGCAGCAGCTGGAGCAATGCGACGTCCCCGAGGACGTGCGGGTTGGCTGCATGACCACAGACTTCGCCAGG
CAGAATGTTCTGCTGCAGATGGGGCTGCACCTGCTGGCGGTGAACTGCATGCTGATTCGTGAGGCCCGGAGCTACGTCTT
GGCTGACACGGCTGTTTCAAGACAAAGTCTGACATGAGCCGAGTGTTCTGTTCACACTGTTGGGAACAAGACCCTGAAGA
AAGTGTCCGTGACCATCAGCGACGACGGCACCCTGCACATGCACTTCTCCCGCAACCCCAAGGTGCTGAACGCCCGCGGC
CTCCGGTACTCGCTTCCCACTCCCAAAGGGGGCAAATACGCCATCAACCCCCATCTCACCGAGGATCAGCGCTTCCCTCA
ACCGCAACTCTCCCGAAAGGCCGGGCAGAAAACCAACGTATTCGCCCCTGACTACATCGCTGGGATGTCGCCCTTTGTCA
AGAATGACATCTCCAGCCGCTCGGCTACCCTACAGGTCCGGGACAGCACCTTGGGAGCTGGGCGGAGACGCTTAAATCCC
AACGCTTCCAGAAAGAAGTTTGTGAAGAAAAGG

Alignment

ORF - retro_ptro_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPVEHVVADAGAFLRDAALQDIGKNIYTIREVVTEIRDKATRRRLAVLPYELRFKEPLPEYVRLVTEFS
          MAPV.HVV.DAGAFLRDAALQDIGKNIYTIREVVTEIRDKAT.RRLAVLPYELRFKEP..EYVRLVTEFS
Retrocopy MAPV*HVVGDAGAFLRDAALQDIGKNIYTIREVVTEIRDKATCRRLAVLPYELRFKEPSLEYVRLVTEFS

Parental  KKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVKVSSSIQHPETPLHISGFHLPYKPKPPQET
          KKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVKVS.SIQHPETPLHISGFHLP.KPKPPQET
Retrocopy KKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVKVSLSIQHPETPLHISGFHLPSKPKPPQET

Parental  EKAHSACEPENLEFSSFMFWRNPLPNIDHELQELLIDRGEDVPSEEEEEEENGFEDRKDDSDDDGGGWIT
          EK.H.ACEPENLEFSSFMFWRNPLPNIDHELQE.LIDRGEDVPS.EEEE.ENG.EDRKDDSDDDGGGWIT
Retrocopy EKGHPACEPENLEFSSFMFWRNPLPNIDHELQEPLIDRGEDVPS-EEEEKENGSEDRKDDSDDDGGGWIT

Parental  PSNIKQIQQELEQCDVPEDVRVGCLTTDFAMQNVLLQMGLHVLAVNGMLIREARSYILRC-HGCFKTTSD
          PSNIKQIQQ.LEQCDVPEDVRVGC.TTDFA.QNVLLQMGLH.LAVN.MLIREARSY.L...HGCFKT.SD
Retrocopy PSNIKQIQQQLEQCDVPEDVRVGCMTTDFARQNVLLQMGLHLLAVNCMLIREARSYVLAD<HGCFKTKSD

Parental  MSRVFCSHC-GNKTLKKVSVTVSDNGTLHMHFSRNPKVLNPRGLRYSLPTPKGGKYAINPHLTEDQRFPQ
          MSRVFCSHC.GNKTLKKVSVT.SD.GTLHMHFSRNPKVLN.RGLRYSLPTPKGGKYAINPHLTEDQRFPQ
Retrocopy MSRVFCSHC>GNKTLKKVSVTISDDGTLHMHFSRNPKVLNARGLRYSLPTPKGGKYAINPHLTEDQRFPQ

Parental  LRLSRKARQKTNVFAPDYIAGVSPFVENDISSRSATLQVRDSTLGAGRRRLNPNASRKKFVKKR
          ..LSRKA.QKTNVFAPDYIAG.SPFV.NDISSRSATLQVRDSTLGAGRRRLNPNASRKKFVKKR
Retrocopy PQLSRKAGQKTNVFAPDYIAGMSPFVKNDISSRSATLQVRDSTLGAGRRRLNPNASRKKFVKKR

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	0.18 RPM	26.13 RPM
SRP007412_cerebellum	0.00 RPM	28.07 RPM
SRP007412_heart	0.06 RPM	10.41 RPM
SRP007412_kidney	0.00 RPM	26.31 RPM
SRP007412_liver	0.07 RPM	32.64 RPM
SRP007412_testis	0.00 RPM	10.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2019 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2019 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2984
Gorilla gorilla	retro_ggor_2067

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014384	1 retrocopy	retro_eeur_450,
Homo sapiens	ENSG00000141101	1 retrocopy	retro_hsap_2984,
Gorilla gorilla	ENSGGOG00000025456	1 retrocopy	retro_ggor_2067,
Pan troglodytes	ENSPTRG00000008285	1 retrocopy	retro_ptro_2019 ,