RetrogeneDB ID: retro_ptro_1057

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:53317870..53319244(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT6L
• Ensembl ID: ENSPTRG00000016198
• Aliases: None
• Description: None

Sequence

>retro_ptro_1057
CTGGGCAGAATTAGAAATCTCGGGGAATTGCTTTTAAATAACAATCTGTTACGGGTTTTGCCTTATGAACTTGGTCGGCT
CTTCCAGCTACAAACTCTAGGTTTGAAAGGCAATCCTTTATCACAGGATATTCTCAACTTATACCAGGGCCCAGATGGAA
CCCGAAAGCTACTGAACTTCATGCTTGACAATCTGGCAGTTCATCCAGAGCAGCTTCCTCCGAGGCCATGGATTACATTA
AAAGAACGAGACCAAATTCTGCCATCAGCATCATTCACGGTTATGTGTTACAATGTGTTATGTGATAAATACGATACCCG
GCAGCTATATGGTTATTGCCCATCCTGGGCATTAAACTGGGAATACAGGAAAAAGGGAATTATGGAAGAAATTGTTAACT
GTGACGCAGATATCATTAGTCTTCAGGAAGTGGAAACAGAGCAATACTTCACTCTCTTTCTGCCAGCATTGAAGGAGCGT
GAATATGATAGATTTTTTTCTCCAAAGTCACGTGCCAAAATCATGTCTGAGCAGGAGAGAAAGCATGTAGATGGTTGTGC
AATATTCTTCAAAACAGAAAAATTTACATTGGTGCAGAAGCATACAGTGGAATTTAACCAAGTGGCAATGGCTAATTCAG
ATGGATCCGAAGCTATGCTGAACAGAGTGATGACAAAAGATAACATTGGTGTCACTGTGGTATTAGAGGTCCACAAAGAA
CTATTTGGAGCAGGTGTGAAGCCTATTCATGCTGCAGACAAACAGCTGCTTATAGTGGCAAATGCCCACATGCATTGGGA
CCCAGAGTATTCTGATGTGAAGCTCATCCAGACCATGATGTTTGTCTCAGAGGTTAAAACCATTCTGGAGAAAGCCTCTA
GTAGGTCTGGCAGCCCAACTGCAGATCCTACTTCCATCCCGCTGGTGCTATGTGCAGATCTTAACTCATTGCCAGATTCA
GGTGTTGTGGAATACTTAAGCAATGGAGGAATAGCTGACAACCATAAAGACTTCAAGGAACTAAGGTACAATGAGTGTCT
TATGAACTTCAGCTGCAATGGAAAGAATGTAAGCTCAGAAGGGAGAATCACACATGGCTTCCAACTTAAGAGCGCCTATG
AAAATACCTTGATGCCTTACACCAATTACACCTTTGATTTCAAAGGCGTGATTGACTACATTTTCTATTCCAAGACTCAT
TTGAACGTGCTTGGTGTCCTGGGGCCTTTAGATCCTCAATGGCTGGTTGAGAACAACATTACTGGGTGTCCACACCCTCA
TATCCCTTCAGACCACTTCTTAATGTTAACACAACTTGAACTCCACCCTCCACTCCTGCCTCTTGTCAATGGTGTTCACT
TGCCTAATCGGAGG

Alignment

ORF - retro_ptro_1057 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.63 %
• Parental protein coverage: 82.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGNMVSLRELLLNNNLLRVLPYELGRLFQLQTLGLKGNPLSQDILNLYQDPDGTRKLLNFMLDNLAVHPE
          LG....L.ELLLNNNLLRVLPYELGRLFQLQTLGLKGNPLSQDILNLYQ.PDGTRKLLNFMLDNLAVHPE
Retrocopy LGRIRNLGELLLNNNLLRVLPYELGRLFQLQTLGLKGNPLSQDILNLYQGPDGTRKLLNFMLDNLAVHPE

Parental  QLPPRPWITLKERDQILPSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIIS
          QLPPRPWITLKERDQILPSASFTVMCYNVLCDKY.TRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIIS
Retrocopy QLPPRPWITLKERDQILPSASFTVMCYNVLCDKYDTRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIIS

Parental  LQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAM
          LQEVETEQYFTLFLPALKER.YD.FFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAM
Retrocopy LQEVETEQYFTLFLPALKEREYDRFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAM

Parental  ANSDGSEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMM
          ANSDGSEAMLNRVMTKDNIGV.VVLEVHKELFGAG.KPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMM
Retrocopy ANSDGSEAMLNRVMTKDNIGVTVVLEVHKELFGAGVKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMM

Parental  FVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKELRYNECLMNF
          FVSEVK.ILEKASSR.GSPTADP.SIPLVLCADLNSLPDSGVVEYLSNGG.ADNHKDFKELRYNECLMNF
Retrocopy FVSEVKTILEKASSRSGSPTADPTSIPLVLCADLNSLPDSGVVEYLSNGGIADNHKDFKELRYNECLMNF

Parental  SCNGKNGSSEGRITHGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNI
          SCNGKN.SSEGRITHGFQLKSAYEN.LMPYTNYTFDFKGVIDYIFYSKTH.NVLGVLGPLDPQWLVENNI
Retrocopy SCNGKNVSSEGRITHGFQLKSAYENTLMPYTNYTFDFKGVIDYIFYSKTHLNVLGVLGPLDPQWLVENNI

Parental  TGCPHPHIPSDHFSLLTQLELHPPLLPLVNGVHLPNRR
          TGCPHPHIPSDHF..LTQLELHPPLLPLVNGVHLPNRR
Retrocopy TGCPHPHIPSDHFLMLTQLELHPPLLPLVNGVHLPNRR

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	0.20 RPM	19.43 RPM
SRP007412_cerebellum	0.32 RPM	36.74 RPM
SRP007412_heart	0.12 RPM	17.95 RPM
SRP007412_kidney	0.13 RPM	39.23 RPM
SRP007412_liver	0.00 RPM	15.09 RPM
SRP007412_testis	0.11 RPM	23.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1057 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1057 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1570

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138767	1 retrocopy	retro_hsap_1570,
Pan troglodytes	ENSPTRG00000016198	1 retrocopy	retro_ptro_1057 ,