RetrogeneDB ID: retro_ptro_3170

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:134931798..134932914(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC1
• Ensembl ID: ENSPTRG00000018523
• Aliases: None
• Description: None

Sequence

>retro_ptro_3170
ATGGCTCAGCACTTCTCCCTGGACGCCTGCGATGTGGTCGGATTCTACCTGGACCACACCCTGTGTCACTACAACCTGCC
CGAGAGCGCCCCAATCATTTATAATAGCTTTGCCCAGTTCTTAGTTAAGGAGAAAGGGTATGATAAGGAATTGCTCAATG
TGACCCCAGAGGATTGGAATTTCTGTTGCAAGGGTTTGGCATTGGATCTAGAAGATAGGAACTTCCTTAAACTTGCTGAT
AATGGCACTGTTCTCAGGGCAAGCCATGGCACCAAGATGATGACTCCAGAGGTGCTGGCAGAGACATATGGCAAGAAAGG
GTGGAAGCATTTCTTGTCGGACACTGGAATGGCTTGCTGCTCATGAAAGTATTATTTTTACAACTACTTTGACCTGCCAG
GAGCTCTTCTATGTACCAGGGTGGTGGACTATTTAACAACAAACAATGGTCAAAAAACATTTGATTTTTGGAAGGATATA
GTTGCTGCTATACAACACAATTATAAAATGTCAGCTTTTAAGGAAAACTGTGGAATATATATTCCAGAAGTAAAAAGAGA
TCCAGGCAGATATTTACACAGTTGTCCTAAATCTGTGAAAAAATGGTTTCGACAGCTAAAGAATGCTGGGAAAATTCTTC
TGTTAATTACCAGTTCTCACAGTGATTACTGTAGACTTCTCTGCGAATATATCCTCGGGAATGATTTTGCAGACCTTTTT
GACATTGTGATTACAAATGCATTGAAGCCTGGTTTCTTCTCCCACTTACCAAGTCAGAGACCTTTCTGGATGCAGAGAAT
GATGAGGAGCAGGAGGCGCTGCCATCTCTGGATAAACCTGGCTGGTGCTCCCAAGGGAACGCTGTCCACCTCTATGAACT
TCTGAAGAAAATCAATGGCAAACCTGAACCCAAGGTTGTTTATTACGGCATGCATTCAGATATTTTCCTGGCTCATCACT
ATAGTAATTGGGAGACAGTTCTTATCCTGGAAGAACTCAGAGGGATGAAGGTGCAAGGAGTCAGAGGCCTGAGAAGTCAG
AGCCTCTAGAGAAAAAGGAAAATATGAGGGACCAAAGGCAAAGCCTCTAAATACTTCATCTAAAAAATGAGGCTCC

Alignment

ORF - retro_ptro_3170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 82.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQHFSLAACDVVGFDLDHTLCRYNLPESAPLIYNSFAQFLVKEKGYNKELLNVTPEDWDFCCKGLALDL
          MAQHFSL.ACDVVGF.LDHTLC.YNLPESAP.IYNSFAQFLVKEKGY.KELLNVTPEDW.FCCKGLALDL
Retrocopy MAQHFSLDACDVVGFYLDHTLCHYNLPESAPIIYNSFAQFLVKEKGYDKELLNVTPEDWNFCCKGLALDL

Parental  EDGNFLKLANNGTVLRASHGTKMMTPEVLAEAYGKKEWKHFLSDTGMACRSGKYYFYDNYFDLPGALLCA
          ED.NFLKLA.NGTVLRASHGTKMMTPEVLAE.YGKK.WKHFLSDTGMAC.S.KYYFY.NYFDLPGALLC.
Retrocopy EDRNFLKLADNGTVLRASHGTKMMTPEVLAETYGKKGWKHFLSDTGMACCS*KYYFY-NYFDLPGALLCT

Parental  RVVDYLTKLNNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIYFPEIKRDPGRYLHSCPESVKKWLRQLKN
          RVVDYLT..NNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIY.PE.KRDPGRYLHSCP.SVKKW.RQLKN
Retrocopy RVVDYLT-TNNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIYIPEVKRDPGRYLHSCPKSVKKWFRQLKN

Parental  AGKILLLITSSHSDYCRLLCEYILGNDFTDLFDIVITNALKPGFFSHLPSQRP-FRTLENDEEQEALPSL
          AGKILLLITSSHSDYCRLLCEYILGNDF.DLFDIVITNALKPGFFSHLPSQRP.F...ENDEEQEALPSL
Retrocopy AGKILLLITSSHSDYCRLLCEYILGNDFADLFDIVITNALKPGFFSHLPSQRP<FLDAENDEEQEALPSL

Parental  DKPGWYSQGNAVHLYELLKKMTGKPEPKVVYFGDSMHSDIFPARHYSNWETVLILEELRG-DEGTRSQRP
          DKPGW.SQGNAVHLYELLKK..GKPEPKVVY.G..MHSDIF.A.HYSNWETVLILEELRG.DEG.RSQRP
Retrocopy DKPGWCSQGNAVHLYELLKKINGKPEPKVVYYG--MHSDIFLAHHYSNWETVLILEELRG<DEGARSQRP

Parental  EESEPLEK-KGKYEGPKAKPLNTSSKKWGS
          E.SEPLEK.KGKYEGPKAKPLNTSSKK.GS
Retrocopy EKSEPLEK<KGKYEGPKAKPLNTSSKK*GS

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	16.00 RPM
SRP007412_cerebellum	0.04 RPM	8.35 RPM
SRP007412_heart	0.00 RPM	17.49 RPM
SRP007412_kidney	0.03 RPM	35.64 RPM
SRP007412_liver	0.00 RPM	14.24 RPM
SRP007412_testis	0.11 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3170 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3170 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4759
Pongo abelii	retro_pabe_3703

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000178425	1 retrocopy	retro_hsap_4759,
Myotis lucifugus	ENSMLUG00000008313	1 retrocopy	retro_mluc_306,
Nomascus leucogenys	ENSNLEG00000013080	1 retrocopy	retro_nleu_2344,
Pongo abelii	ENSPPYG00000016943	1 retrocopy	retro_pabe_3703,
Pan troglodytes	ENSPTRG00000018523	1 retrocopy	retro_ptro_3170 ,