RetrogeneDB ID: retro_pabe_3703

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:133720100..133721014(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC1
• Ensembl ID: ENSPPYG00000016943
• Aliases: None
• Description: 5'-nucleotidase domain containing 1 [Source:HGNC Symbol;Acc:21556]

Sequence

>retro_pabe_3703
ATGGCTCAGCACTTCTCCCCGGACACCTGCAACGTGGTCGGATTCTACCTGGACCACACCCTGTGTCACTACAACCTGCC
CGAGAGCGCCCCACTCATTTATAATAGCTTTGCCCAGTTCTTAGTTAAGGAGAAAGGGTATGATAAGGAATTGCTCAATG
TGACCCCAGAGGATTGGAATTTCTGTTGCAAGGATTTGGCATTGGATCTAGAAGATAAGAACTTCCTTAAACTTGCTGAT
AATGGCACTGTTCTCAGGGCAAGCTATGGCACCAAGATGATGACTCCAGAGGTGCTGGCAGAGACATATGGCAAGAAAGG
TGGAAGCACTTCTTGTCGGACACTGGAATGGCTTGCCGCTCATGAAAGTATTATTTTTACAACTACATTGACCTTCCAGG
AGCTCTTCTATGTGCCAGGGTGGTGGACTATTTAACAACAAACAATGGTCAAAAAACATTTGATTTTTGGAAGGATATAG
TTGCTGCTATACAACACAATTATAAAATGTCAGCTTTTAGGGAAAACTGTGGAATATATTTTCCAGAAGTAAAAAGAGAT
CCAGGCAGATATTTACACAGTTGTCCTGAATCTGTGAAAAAAATGGCTTTGACAGCTAAAGAATGCTGGGAAAATTCTTC
TGTTAATTACCAGTTCTCACAGTGATTACTGTAGACTTCTCTGTGAATATATCCTTGGGAATGATTTTGCAGAACTTCTT
GACATTGTGATTACAAATGCATTGAAGCCTGGTTTCTTCTCCCACTTACCAAGTCAGAGACCTTTCTAGATGCAGAGAAT
GATGAGGAGCAGGAGGTGCTGCCATATCTGGATAAACCTGGCTGGTGCTCCCAAGGGAACGCTGTCCACCCCTATGAACT
TCTGAAGAAAATCACTGGCAAACCTGAACCCAAG

Alignment

ORF - retro_pabe_3703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 76.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQHFSLAACDVVGFDLDHTLCRYNLPESAPLIYNSFAQFLVKEKGYDKELLNVTPEDWDFCCKGLALDL
          MAQHFS...C.VVGF.LDHTLC.YNLPESAPLIYNSFAQFLVKEKGYDKELLNVTPEDW.FCCK.LALDL
Retrocopy MAQHFSPDTCNVVGFYLDHTLCHYNLPESAPLIYNSFAQFLVKEKGYDKELLNVTPEDWNFCCKDLALDL

Parental  EDGNFLKLANNGTVLRASHGTKMMTAEVLAEAYGKK-EWKHFLSDTGMACRSGKYYFYDNYFDLPGALLC
          ED.NFLKLA.NGTVLRAS.GTKMMT.EVLAE.YGKK..WKHFLSDTGMACRS.KYYFY.NY.DLPGALLC
Retrocopy EDKNFLKLADNGTVLRASYGTKMMTPEVLAETYGKK<RWKHFLSDTGMACRS*KYYFY-NYIDLPGALLC

Parental  ARVVDYLTKQNNGQKTFDFWKDIVAAIQHNYKMSAFKENCGIYFPEIKRDPGRYLHSCPESV-KKWLRQL
          ARVVDYLT..NNGQKTFDFWKDIVAAIQHNYKMSAF.ENCGIYFPE.KRDPGRYLHSCPESV.KKWL.QL
Retrocopy ARVVDYLT-TNNGQKTFDFWKDIVAAIQHNYKMSAFRENCGIYFPEVKRDPGRYLHSCPESV>KKWL*QL

Parental  KNAGKILLLITSSHSDYCRLLCEYILGNDFTDLFDIVITNALKPGFFSHLPSQRP-FRTLENDEEQEALP
          KNAGKILLLITSSHSDYCRLLCEYILGNDF..L.DIVITNALKPGFFSHLPSQRP.F...ENDEEQE.LP
Retrocopy KNAGKILLLITSSHSDYCRLLCEYILGNDFAELLDIVITNALKPGFFSHLPSQRP<FLDAENDEEQEVLP

Parental  SLDKPGWYSQGNAVHLYELLKKMTGKPEPK
          .LDKPGW.SQGNAVH.YELLKK.TGKPEPK
Retrocopy YLDKPGWCSQGNAVHPYELLKKITGKPEPK

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	0.00 RPM	3.37 RPM
SRP007412_cerebellum	0.12 RPM	5.23 RPM
SRP007412_heart	0.03 RPM	9.54 RPM
SRP007412_kidney	0.13 RPM	8.55 RPM
SRP007412_liver	0.06 RPM	7.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3703 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3703 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4759
Pan troglodytes	retro_ptro_3170

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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,