RetrogeneDB ID: retro_ptro_2057

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:67081319..67082452(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOC5
• Ensembl ID: ENSPTRG00000023297
• Aliases: None
• Description: None

Sequence

>retro_ptro_2057
CAGACTTTCTTGTCTAAGCTTATCAAATCCATATTCATTTCCTATTTGGAGAACTATGTTGAGGTGGAGACTAGATATTT
GAAAAGCAGAAGTGCTATGATCCTACAGCGCTATTATGATTTGAAAAACCATCAGAAGAGATCCATTGGCACAGGAGGTA
TTCAAGATTTGAAGGAGAGAATTAGACAACACACCAACTTACCACTTGGGCCAAGTATGGATACTTATGGGGAAACTTTT
CTATCCCAAGAAGTGGTGGTTAATCTTTTACAAGAAACCCGACAAGCCTTTGAAAGATGTCATAGGCTCTCTGATCCTTC
TGACTTGCCAGGGAATGCCTTCAGAATTTTTACCTTCTCGTGGAATTTTTATGTATTGAGCATATTGATTATGCTTTGGA
AACAGGACTTGCTGGAATTCCCTCTTCAGATTCTAGGAATGCAAATCTTTATTTTTTGGATGTTGTGCAACAGGCCAATA
CTATTTTTCATCTTTTTGACAAACAGTTTAATGATCACCTTATGCCACTAATAAGCTCTTCTCCTAAGTTATCTGAATGC
CTTCAGAAGAAAAAAGGAATAATTGAACAAATGGAGATGAAATTGGATACTGGCATTGATAGGACATTAAATTGTATGAT
TGGACAGATGAAGCATATTTTGGCTGCAGAACAAAAGAAAACAGATTTTAAGCCAGAAGATGAAAACAATGTTTTGATTC
AATATACTAATGCCTGTGTAAAAGTCTGTGCTTATGTAAGAAAACAAGTGGAGAAGATTAAAAATTCCATGGATGGGAAG
AATGTGGATACAGTTTTGATGGAACTTGGAGTACGTTTTCATCGACTTATCTATGAGCATCTTCAACAATATTCCTACAG
TTATATGGGTGGCATGTTGGCAATTTGCGATGTAGCTGAATATAGGAAGTGTGCCAAAGACTTCAAGATTCCAATGGTAT
TACATCTTTTTGATACTCTGCATGCTCTTTGCAATCTTCTGGTAGTTGCCCCAGATGATTTAAAGCAAGTCTGCTCAGGA
GAACAACTTGCTAATTTGGACAAGAATATACTTCACTCCTTCGTACAACTTTGTGCTGATTATAGATCTGCCCGCCTTGC
TCGACACTTCAAC

Alignment

ORF - retro_ptro_2057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 53.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTFLSKLIKSIFISYLENYIEVETGYLKSRSAMILQRYYDSKNHQKRSIGTGGIQDLKERIRQRTNLPLG
          QTFLSKLIKSIFISYLENY.EVET.YLKSRSAMILQRYYD.KNHQKRSIGTGGIQDLKERIRQ.TNLPLG
Retrocopy QTFLSKLIKSIFISYLENYVEVETRYLKSRSAMILQRYYDLKNHQKRSIGTGGIQDLKERIRQHTNLPLG

Parental  PSIDTHGETFLSQEVVVNLLQETKQAFERCHRLSDPSDLPRNAFRIFT-ILVEFLCIEHIDYALETGLAG
          PS.DT.GETFLSQEVVVNLLQET.QAFERCHRLSDPSDLP.NAFRIFT..LVEFLCIEHIDYALETGLAG
Retrocopy PSMDTYGETFLSQEVVVNLLQETRQAFERCHRLSDPSDLPGNAFRIFT<LLVEFLCIEHIDYALETGLAG

Parental  IPSSDSRNANLYFLDVVQQANTIFHLFDKQFNDHLMPLISSSPKLSECLQKKKEIIEQMEMKLDTGIDRT
          IPSSDSRNANLYFLDVVQQANTIFHLFDKQFNDHLMPLISSSPKLSECLQKKK.IIEQMEMKLDTGIDRT
Retrocopy IPSSDSRNANLYFLDVVQQANTIFHLFDKQFNDHLMPLISSSPKLSECLQKKKGIIEQMEMKLDTGIDRT

Parental  LNCMIGQMKHILAAEQKKTDFKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVR
          LNCMIGQMKHILAAEQKKTDFKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVR
Retrocopy LNCMIGQMKHILAAEQKKTDFKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVR

Parental  FHRLIYEHLQQYSYSCMGGMLAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPDNLKQVCSGEQ
          FHRLIYEHLQQYSYS.MGGMLAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPD.LKQVCSGEQ
Retrocopy FHRLIYEHLQQYSYSYMGGMLAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPDDLKQVCSGEQ

Parental  LANLDKNILHSFVQLRADYRSARLARHFS
          LANLDKNILHSFVQL.ADYRSARLARHF.
Retrocopy LANLDKNILHSFVQLCADYRSARLARHFN

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	0.05 RPM	27.19 RPM
SRP007412_cerebellum	0.04 RPM	23.88 RPM
SRP007412_heart	0.12 RPM	35.62 RPM
SRP007412_kidney	0.05 RPM	38.18 RPM
SRP007412_liver	0.00 RPM	15.42 RPM
SRP007412_testis	0.63 RPM	167.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2057 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2057 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2938
Pongo abelii	retro_pabe_2517

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000070367	1 retrocopy	retro_hsap_2938,
Oryctolagus cuniculus	ENSOCUG00000000756	1 retrocopy	retro_ocun_1593,
Pongo abelii	ENSPPYG00000005848	1 retrocopy	retro_pabe_2517,
Pan troglodytes	ENSPTRG00000023297	1 retrocopy	retro_ptro_2057 ,