RetrogeneDB ID: retro_hsap_1570

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:56297910..56299245(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000230183
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNOT6L
• Ensembl ID: ENSG00000138767
• Aliases: CNOT6L, CCR4b
• Description: CCR4-NOT transcription complex, subunit 6-like [Source:HGNC Symbol;Acc:18042]

Sequence

>retro_hsap_1570
AATTGCTTGTTACGGGTTTTGCCTTATGAACTTGGTGGGCTCTTCCAGCTACAAACTCTAGGTTTGAAAGGCAATCCTTT
ATCACAGGATATTCTCAACTTATACCAGGACCCAGATGGAACCCGAAATCTACTGAACTTCATGCTTGACAATCTCGCAG
TTCATCCAGAGCAGCTTCCTCCGAGGCCATGGATTACATTAAAAGAACGAGACCAAATTCTGCCATCAGCATCATTCACG
GTTATCTGTTACAATGTGTTATGTGATAAATACGCTACCCGGCAGCTATATGGTTATTGCCCATCCTGGGCATTAAACTT
GGAATACAGGAAAAAGGGAATTATGGAAGAAATTGTTAACTGTGACGCAGATATCATTAGTCTTCAGGAAGTGGAAACAG
AGCAATACTTCACTCTCTTTCTGCCAGCATTGAAGGAGCGTGAATATGATGGATTTTTTTCTCCAAAGTCACGTGCCAAA
ATCATGTCTGAGCAGGAGAGAAAGCATGTAGATGGTTGTGCAATATTTTTCAAAAGAGAAAAATTTACATTGGTGCAGAA
GCATGCAGTGGAATTTAACCAAGTGGCAATGGCTAATTCAGATGGATCCGAAGCTATGCTGAACAGAGTGATGACAAAAG
ATAACATTGGTGTCACTGTGGTATTAGAGGTCCACAAAGAACTATTTGGAGCAGGTATGAAGCCTATTCATGCTGCAGAC
AAACAGCTGCTTATAGTGGCAAATGCCCACATGCATTGGGACCCAGAGTATTCTGATGTGAAGCTCATCCAGACCATGAT
GTTTGTCTCAGAGGTTAAAACCATTCTGGAGAAAGCCTCTAGTAGGTCTGGCAGCCCAACTGCAGATCCTAATTCCATCC
CGCTGGTGCTATGTGCAGATCTTAACTCATTGCCAGATTCAGGTGTTGTGGAATACTTAAGCAATGGAGGAATAGCTGAC
AACCATAAAGACTTCAAGGAACTAAGGTACAATAAGTGTCTTATGAACTTCAGCTGCAATGGAAAGAATGGAAGCTCAGA
AGGGAGAATCACACATGGCTTCCAACTTAAGAGCGCCTACGAAAATAACTTGATGCCTTACACCAATTACACCTTTGATT
TCAAAGGCGTGATTGACTACATTTTCTATTCCAAGACTCATATGAATGTGCTTGGTGTCCTGGGGCCTTTAGATCCTCAA
TGGCTGGTTGAGAACAACATCACTGGGTGTCCACACCCTCACATCCCTTCAGACCACTTCTCACTGTTAACACAACTTGA
ACTCCACCCTCCACTCCTGCCTCTTGTCAATGGTGTTCACTTGCCTAATCGGAGG

Alignment

ORF - retro_hsap_1570 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 79.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NNLLRVLPYELGRLFQLQTLGLKGNPLSQDILNLYQDPDGTRKLLNFMLDNLAVHPEQLPPRPWITLKER
          N.LLRVLPYELG.LFQLQTLGLKGNPLSQDILNLYQDPDGTR.LLNFMLDNLAVHPEQLPPRPWITLKER
Retrocopy NCLLRVLPYELGGLFQLQTLGLKGNPLSQDILNLYQDPDGTRNLLNFMLDNLAVHPEQLPPRPWITLKER

Parental  DQILPSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLF
          DQILPSASFTV.CYNVLCDKYATRQLYGYCPSWALN.EYRKKGIMEEIVNCDADIISLQEVETEQYFTLF
Retrocopy DQILPSASFTVICYNVLCDKYATRQLYGYCPSWALNLEYRKKGIMEEIVNCDADIISLQEVETEQYFTLF

Parental  LPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRV
          LPALKER.YDGFFSPKSRAKIMSEQERKHVDGCAIFFK.EKFTLVQKH.VEFNQVAMANSDGSEAMLNRV
Retrocopy LPALKEREYDGFFSPKSRAKIMSEQERKHVDGCAIFFKREKFTLVQKHAVEFNQVAMANSDGSEAMLNRV

Parental  MTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKAS
          MTKDNIGV.VVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVK.ILEKAS
Retrocopy MTKDNIGVTVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKTILEKAS

Parental  SRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRI
          SR.GSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGG.ADNHKDFKELRYN.CLMNFSCNGKNGSSEGRI
Retrocopy SRSGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGIADNHKDFKELRYNKCLMNFSCNGKNGSSEGRI

Parental  THGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHF
          THGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHF
Retrocopy THGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHF

Parental  SLLTQLELHPPLLPLVNGVHLPNRR
          SLLTQLELHPPLLPLVNGVHLPNRR
Retrocopy SLLTQLELHPPLLPLVNGVHLPNRR

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
bodymap2_adipose	0.12 RPM	149.72 RPM
bodymap2_adrenal	0.02 RPM	103.04 RPM
bodymap2_brain	0.14 RPM	53.14 RPM
bodymap2_breast	0.02 RPM	81.27 RPM
bodymap2_colon	0.19 RPM	96.20 RPM
bodymap2_heart	0.04 RPM	30.41 RPM
bodymap2_kidney	0.00 RPM	76.68 RPM
bodymap2_liver	0.00 RPM	27.57 RPM
bodymap2_lung	0.19 RPM	134.99 RPM
bodymap2_lymph_node	0.00 RPM	123.58 RPM
bodymap2_ovary	0.02 RPM	77.40 RPM
bodymap2_prostate	0.16 RPM	82.89 RPM
bodymap2_skeletal_muscle	0.00 RPM	46.03 RPM
bodymap2_testis	0.11 RPM	84.22 RPM
bodymap2_thyroid	0.02 RPM	86.64 RPM
bodymap2_white_blood_cells	0.04 RPM	282.87 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1570 was not detected

EST

1 EST(s) were mapped to retro_hsap_1570 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EL593823	56297781	56298487	98.9	688	3	681

TSS

No TSS is located nearby retro_hsap_1570 retrocopy 5' end.

Lab

retro_hsap_1570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1570 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1057

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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,