RetrogeneDB ID: retro_pabe_598

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:64891561..64892734(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CEP57L1
• Ensembl ID: ENSPPYG00000016901
• Aliases: None
• Description: centrosomal protein 57kDa-like 1 [Source:HGNC Symbol;Acc:21561]

Sequence

>retro_pabe_598
ATGGATTCTGAATTAATGCATAGTATAGTAGGAAGCTATCATAAACCTCCAGAAAGAGTATTCGTTCCCTCATTCACCCA
GAATGAACCATCTCAGAATTGCCATCTTGCGAACTTAGAAGTTACCTCTCCTAAGATACTTCATAGCCCAAATAGCCAAG
CTCTTATTTTAGCCTTAAAAACTCTTCAGGAAAAAATTCATTGTTTAGAGCTGGAGAGAACACAAGCTGAAGATAACCTG
AACATTCTTTCCAGAGAAGCAGCACAGTATAAGAAGGCCTTAGAGAATGAAACAAATGAGAGAAATCTGGCACATCAGGA
GCTGATAAAGCAGAAAAAAGATATAAGTATACAGTTAAGCTCAGCCCAGTCTCGTTGCACTCTTCTAGAGAAGCAACTAG
AATATACAAAGAGAATGGTTCTCAATGGAGAGCGAGAAAAGAACATGATCCTAGAACAACAGGCCCAGCTTCAGAAGGAA
AAAGAGCAAGATCAGATGAAGCTGTATGCAAAACTTGAAAAGCTTGATGTCTTAGAAAAAGAGTGTTTTAGACTTACAAC
AACTCAGAGAACTGCTGAGGACAAGATTAAACATTTAGAAGAAAAACTTAAGGAAGAAGAACATCAATGTAAGCTATTTC
AAGACAAAGCTTCTGAGCTTCAAACTGGACTTGAAATCAGTAAAATTATAATGCCTTCAGTTTCAAATCTAAAGCACTCC
AAGGAAAAGAAGAAATCTTCAAAGAAAACTAAATATATAAGGAGAGGACCACCTTGGCAAATTTGTTCAAAGTTTGGAGC
ACTGCCTTTTGTGGCTGAAAAGATGAGGCAACATCGTGACCCACATATCCTTCAGAAACCTTTTAACGTGACTGAGACTA
GATGTCTCCCCAAGCCTTCTAGAACAACTTCCTGGTGTAAAGCTATTCCTCCTGACTCAGAAAAGTCCATTTCCATTTGT
GACAATTTATCTGAACTTTTGATGGCAATGCAAGATGAGCTGGACCAAATGAGCATGGAGCACCAAGAACTACTCAAACA
AATGAAGGAAACTGAAAGCCATTCAGTCTGTGACGACATAGAATGTGAACTAGAGTGTCTAGTTAAGAAAATGGAAATTA
AAGGAAAACAAATCTCCAAACTGAAGAAGCATCAAGACAGTGTAAGCAGGCTT

Alignment

ORF - retro_pabe_598 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.4 %
• Parental protein coverage: 85.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSELMHSIVGSYHKPPERVFVQSFTQNEPSQNCHPANLEVTSPKILHSPNSQALILALKTLQEKIHRLE
          MDSELMHSIVGSYHKPPERVFV.SFTQNEPSQNCH.ANLEVTSPKILHSPNSQALILALKTLQEKIH.LE
Retrocopy MDSELMHSIVGSYHKPPERVFVPSFTQNEPSQNCHLANLEVTSPKILHSPNSQALILALKTLQEKIHCLE

Parental  LERTQAEDNLNILSRETAQYKKALENETNERNLAHQELIKQKKDISIQLSSAQSRCTLLEKQLEYTKRMV
          LERTQAEDNLNILSRE.AQYKKALENETNERNLAHQELIKQKKDISIQLSSAQSRCTLLEKQLEYTKRMV
Retrocopy LERTQAEDNLNILSREAAQYKKALENETNERNLAHQELIKQKKDISIQLSSAQSRCTLLEKQLEYTKRMV

Parental  LNVEREKNMILEQQAQLQREKEQDQMKLYAKLEKLDVLEKECFRLTTTQKTAEDKIKHLEEKLKEEEHQR
          LN.EREKNMILEQQAQLQ.EKEQDQMKLYAKLEKLDVLEKECFRLTTTQ.TAEDKIKHLEEKLKEEEHQ.
Retrocopy LNGEREKNMILEQQAQLQKEKEQDQMKLYAKLEKLDVLEKECFRLTTTQRTAEDKIKHLEEKLKEEEHQC

Parental  KLFQDKASELQTGLEISKIIMSSVSNLKHFKERKKSSKKTKCIKRGPPWQICSKFGALPFVAEKMRQHRD
          KLFQDKASELQTGLEISKIIM.SVSNLKH.KE.KKSSKKTK.I.RGPPWQICSKFGALPFVAEKMRQHRD
Retrocopy KLFQDKASELQTGLEISKIIMPSVSNLKHSKEKKKSSKKTKYIRRGPPWQICSKFGALPFVAEKMRQHRD

Parental  PHILQKPFNVTETRCLPKPSRTTSWCKAIPPDSEKSISICDNLSELLMAMQDELDQMSIEHQELLKQMKE
          PHILQKPFNVTETRCLPKPSRTTSWCKAIPPDSEKSISICDNLSELLMAMQDELDQMS.EHQELLKQMKE
Retrocopy PHILQKPFNVTETRCLPKPSRTTSWCKAIPPDSEKSISICDNLSELLMAMQDELDQMSMEHQELLKQMKE

Parental  TESHSVCDDIECELECLLKKMEIKGEQISKLKKHQDSVRKL
          TESHSVCDDIECELECL.KKMEIKG.QISKLKKHQDSV..L
Retrocopy TESHSVCDDIECELECLVKKMEIKGKQISKLKKHQDSVSRL

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	0.17 RPM	0.88 RPM
SRP007412_cerebellum	0.00 RPM	1.46 RPM
SRP007412_heart	0.03 RPM	0.84 RPM
SRP007412_kidney	0.00 RPM	1.52 RPM
SRP007412_liver	0.06 RPM	1.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_598 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_598 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_591
Pan troglodytes	retro_ptro_434
Gorilla gorilla	retro_ggor_523

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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,