RetrogeneDB ID: retro_ptro_434

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:68895143..68896310(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CEP57L1
• Ensembl ID: ENSPTRG00000018480
• Aliases: None
• Description: centrosomal protein 57kDa-like 1 [Source:HGNC Symbol;Acc:21561]

Sequence

>retro_ptro_434
ATGGATTCTGAATTAATGCATAGTATAGTAGGAAGCTATCATAAACCTCCAGAAAGAGTATTCGTTCCCTCATTCACCCA
GAATGAACCATCTCAGAATTGCCATCCTGCGAACTTAGAAGTTACCTCTCCTAAGATACTTCATAGCCCAAATAGCCAAG
CTCTTATTTTAGCCTTAAAAACTCTTCAGGAAAAAATGCATTGTTTAGAGCTGGAGAGAACACAAGCTGAAGATAACCTG
AACATTCTTTCCAGAGAAGCAGCACAGTATAAGAAGGCCTTAGAGAATGAAACAAATGAGAGAAATCTGTCACATCAGGA
GCTGATAAAGCAGAAAAAAGATGTAAGTATACAGTTAAGCTCAGCCCAGTCTCGTTGCACTCTTCTAGAGAAGCAACTAG
AATATACAAAGAGAATGGTTCTCAATGTAGAGCGAGAAAAGAACATGATCCTAGAACAACAGGCCCAGCTTCAGAGGGAA
AAAGAACAAGATCAGATGAAGCTGTATGCAAAACTTGACAAGCTTGATGTCTTAGAAAAAGAGTGTTTTAGGCTTACAAC
AACTCAGAAAACTGCTGAGGACAAGATTAAACATTTAGAAGAAAAACTTAAGGACGAAGAACATCAACATAAGCTATTTC
AAGACAAAGCTTCTGAGCTTCAAACTGGACTTGAAATCAGTAAAATTATGTCTTCAGTTTCAAATCTAAAGCACTCCAAG
GAAAAGAAGAAATCTTCAAAGAAAACTAAATGTATAAAGAGAGGACCACCTTGGCAAATTTGTTCAAAGTTTGGAGCACT
GCCTTTTGTGGCTGAAAAGAGGCAACATCGTGACCCACATATCCTTCCGAAATCTTTTAACGTGACTGAGACTAGATGTC
TCCCCAAGCCTTCTAGAACAACTGCCTGGTGTAAAGCTATTACTCCTGACTCAGAAAAGTCCATTTCCATTTGTGACAAT
TTATCTGAACTTTTGATGGCAATGCAAGATGAGCTGGACCAAATGAGCACGGACCACCAAGAACTACTCAAACAAATGAA
GGAAACTGAAAGCCATTCAGTCTGTGACGAGATAGAATGTGAACTAGAGTGTTTAGTCAAGAAAATGGAAATTAAAGGAG
AACAAATCTCCGAACTGAAGAAGCATCAAGACAGTGTAAGAAGGCTT

Alignment

ORF - retro_ptro_434 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 85.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSELMHSIVGSYHKPPERVFVPSFTQNEPSQNCHPANLEVTSPKILHSPNSQALILALKTLQEKIRRLE
          MDSELMHSIVGSYHKPPERVFVPSFTQNEPSQNCHPANLEVTSPKILHSPNSQALILALKTLQEK...LE
Retrocopy MDSELMHSIVGSYHKPPERVFVPSFTQNEPSQNCHPANLEVTSPKILHSPNSQALILALKTLQEKMHCLE

Parental  LERTQAEDNLNILSREAAQYKKALENETNERNLAHQELIKQKKDISIQLSSAQSRCTLLEKQLEYTKRMV
          LERTQAEDNLNILSREAAQYKKALENETNERNL.HQELIKQKKD.SIQLSSAQSRCTLLEKQLEYTKRMV
Retrocopy LERTQAEDNLNILSREAAQYKKALENETNERNLSHQELIKQKKDVSIQLSSAQSRCTLLEKQLEYTKRMV

Parental  LNVEREKNMILEQQAQLQREKEQDQMKLYAKLEKLDVLEKECFRLTTTQKTAEDKIKHLEEKLKEEEHQR
          LNVEREKNMILEQQAQLQREKEQDQMKLYAKL.KLDVLEKECFRLTTTQKTAEDKIKHLEEKLK.EEHQ.
Retrocopy LNVEREKNMILEQQAQLQREKEQDQMKLYAKLDKLDVLEKECFRLTTTQKTAEDKIKHLEEKLKDEEHQH

Parental  KLFQDKASELQTGLEISKIIMSSVSNLKHSKEKKKSSKKTKCIKRRPPWQICSKFGALPFVAEKMRQHRD
          KLFQDKASELQTGLEISK.IMSSVSNLKHSKEKKKSSKKTKCIKR.PPWQICSKFGALPFVAEK.RQHRD
Retrocopy KLFQDKASELQTGLEISK-IMSSVSNLKHSKEKKKSSKKTKCIKRGPPWQICSKFGALPFVAEK-RQHRD

Parental  PHILQKPFNVTETRCLPKPSRTTSWCKAIPPDSEKSISICDNLSELLMAMQDELDQMSMEHQELLKQMKE
          PHIL.K.FNVTETRCLPKPSRTT.WCKAI.PDSEKSISICDNLSELLMAMQDELDQMS..HQELLKQMKE
Retrocopy PHILPKSFNVTETRCLPKPSRTTAWCKAITPDSEKSISICDNLSELLMAMQDELDQMSTDHQELLKQMKE

Parental  TESHSVCDDIECELECLLKKMEIKGEQISKLKKHQDSVCKL
          TESHSVCD.IECELECL.KKMEIKGEQIS.LKKHQDSV..L
Retrocopy TESHSVCDEIECELECLVKKMEIKGEQISELKKHQDSVRRL

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	0.04 RPM	4.20 RPM
SRP007412_cerebellum	0.18 RPM	3.69 RPM
SRP007412_heart	0.15 RPM	2.65 RPM
SRP007412_kidney	0.13 RPM	5.33 RPM
SRP007412_liver	0.03 RPM	2.65 RPM
SRP007412_testis	0.53 RPM	35.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_434 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_434 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_591
Gorilla gorilla	retro_ggor_523
Pongo abelii	retro_pabe_598

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183137	1 retrocopy	retro_hsap_591,
Gorilla gorilla	ENSGGOG00000014982	1 retrocopy	retro_ggor_523,
Nomascus leucogenys	ENSNLEG00000012502	1 retrocopy	retro_nleu_2216,
Otolemur garnettii	ENSOGAG00000015479	1 retrocopy	retro_ogar_902,
Pongo abelii	ENSPPYG00000016901	1 retrocopy	retro_pabe_598,
Pan troglodytes	ENSPTRG00000018480	1 retrocopy	retro_ptro_434 ,