RetrogeneDB ID: retro_pabe_2517

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:57023574..57024708(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOC5
• Ensembl ID: ENSPPYG00000005848
• Aliases: None
• Description: exocyst complex component 5 [Source:HGNC Symbol;Acc:10696]

Sequence

>retro_pabe_2517
CAGACTTTCTTGCCTAAGCTTATCAAATCCATATTCATTTCCTATTTGGAGAACTATATTGAGGTGGAGACTAGATATTT
GAAAAGCAGGAGTGCTATGATCCTACAGCGCTATTATGATTCGAAAAACCATCAAAAGAGATCCATTGGCACAGGAGGTA
TTCAAGATTTGAAGGAGAGAATTAGACAACATACCGACTTACCACTTGGGCCAAGTATCGTTACTCACGGGGAAACTTTT
CTATCCCAAGAAGTGGTGGTTAATCTTTTACAAGAAACCCAGCAAGCCTTCGAAAGATGTCATAGGCTCTCTGATCCTTC
TGACTTACCAGGGAATGCCTTCAGAATTTTTACCGTTCTTGTGGAATTTTTATGTATTGAGCATATTGATTATGCTTTGG
AAACAGGACTTGGTGAAATTCCCTCTTCAGATTCTAGGAATGCAAATCTTTATTTTTTGGATGTTGTGCAACAGGCCAAT
ACTATTTTTCATCTTTTTGACAAACAGTTTAATGATCACCTTATGCCACTAATAAGCTCTTCTCCCAAGTTATCTGAATG
CCTTCAGAAGAAAAAAGAAATAACTGAACAAATGGAGATGAAATTGGATACTGGCATTGATAGGACATTAAATTGTATGA
TTGGACAGACGAAGCATATTTTGGCTGCAGAACAAAAGAAAACAGATTTTAAGCCAGAAGATGAAAACAATGTTTTGATT
CAATAAACTAATGCCTGTGTAAAAGTCTGTGCTTATGTAAGAAAACAAGTGGAGAAGATTAAAAATTCCATGGATGGGAA
GAATGTGGATACAGTTTTGATGGAACTTGGAGTATGTTTTCATCAACTTATCTATGAGCATCTTCAACAATATTCCTACA
GTTGTATGGGTGGCATCTTGGCAATTTGTGATGTAGCTGAATATAGGAAGTGTGCCAAAGACTTCAAGATTCCAATGGTA
TTACATCTTTTTGATACTCTGCATGCTCTTTGCAATCTTCTGGTAGTTGCCCCAGGTAATTTAAAGCAAGTCTGCTCAGG
AAAACAACTTGCTAATTTGGACAAGAATATACTTCACTCCTTTGTACAACTTTGTGCTGATTATAGATCTGCCTGCCTTT
CTCGACACTTCAGC

Alignment

ORF - retro_pabe_2517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.44 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTFLSKLIKSIFISYLENYIEVETGYLKSRSAMILQRYYDSKNHQKRSIGTGGIQDLKERIRQRTNLPLG
          QTFL.KLIKSIFISYLENYIEVET.YLKSRSAMILQRYYDSKNHQKRSIGTGGIQDLKERIRQ.T.LPLG
Retrocopy QTFLPKLIKSIFISYLENYIEVETRYLKSRSAMILQRYYDSKNHQKRSIGTGGIQDLKERIRQHTDLPLG

Parental  PSIDTHGETFLSQEVVVNLLQETKQAFERCHRLSDPSDLPRNAFRIFTILVEFLCIEHIDYALETGLAGI
          PSI.THGETFLSQEVVVNLLQET.QAFERCHRLSDPSDLP.NAFRIFT.LVEFLCIEHIDYALETGL..I
Retrocopy PSIVTHGETFLSQEVVVNLLQETQQAFERCHRLSDPSDLPGNAFRIFTVLVEFLCIEHIDYALETGLGEI

Parental  PSSDSRNANLYFLDVVQQANTIFHLFDKQFNDHLMPLISSSPKLSECLQKKKEIIEQMEMKLDTGIDRTL
          PSSDSRNANLYFLDVVQQANTIFHLFDKQFNDHLMPLISSSPKLSECLQKKKEI.EQMEMKLDTGIDRTL
Retrocopy PSSDSRNANLYFLDVVQQANTIFHLFDKQFNDHLMPLISSSPKLSECLQKKKEITEQMEMKLDTGIDRTL

Parental  NCMIGQMKHILAAEQKKTDFKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVRF
          NCMIGQ.KHILAAEQKKTDFKPEDENNVLIQ.TNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGV.F
Retrocopy NCMIGQTKHILAAEQKKTDFKPEDENNVLIQ*TNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVCF

Parental  HRLIYEHLQQYSYSCMGGMLAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPDNLKQVCSGEQL
          H.LIYEHLQQYSYSCMGG.LAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAP.NLKQVCSG.QL
Retrocopy HQLIYEHLQQYSYSCMGGILAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPGNLKQVCSGKQL

Parental  ANLDKNILHSFVQLRADYRSARLARHFS
          ANLDKNILHSFVQL.ADYRSA.L.RHFS
Retrocopy ANLDKNILHSFVQLCADYRSACLSRHFS

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	0.11 RPM	14.65 RPM
SRP007412_cerebellum	0.00 RPM	19.46 RPM
SRP007412_heart	0.03 RPM	9.69 RPM
SRP007412_kidney	0.10 RPM	9.25 RPM
SRP007412_liver	0.03 RPM	7.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2517 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2517 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2938
Pan troglodytes	retro_ptro_2057

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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,