RetrogeneDB ID: retro_ptro_1104

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:47696857..47697626(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF8
• Ensembl ID: ENSPTRG00000021957
• Aliases: None
• Description: None

Sequence

>retro_ptro_1104
ATGGTTGATATGGATCAACTCATAAACAACTTGGAGGTGCAACTTAATTCAGAAGGTGGCTCAATGCAGATATTCAAGCC
CATCACTGGCCCTACTCAGAGCACAGATCCCCCTGAGATAGAAGCAGAAATAATGTGACTTCTCCACCACTCCTGGATGC
CAACCCCATGGAGAACCCAGCATTGTTTAATGACATCAAGTTTGAGCCCCAGAAGAACTTTTGGCGAGTGATTTCAGCCT
GTCCCCAGTGGAACCAGTTGACTTCTCCTCTCACAAGCCCAAGGCTCCTCTCCACCCTGTTAGCATGCTGCAAGCTCCAG
GACATCCTGCCAAGCCACAGTCTGCTCCCGAGACCCTTGTGGTGTTCACTTCAACATCAGCAAACATTCCTACTATTCTG
ACCACAGGATCTGTCCTGACTCCCTCTCAGGGCACTGGTGGCTAGCAGATCTTACATGTCATTCACAGCATCCCCTCAGT
CTGTCTTCCAAGTAAGATGGATTACCTGAATGCCATCCCAGTGGTGGTGCAGTCTCTGCCCATGGTGTATACTACTTTGC
CTGCAAATGAGGGCCCTGCACCCAATACAGTCCCACTCATTGGAGGAGATGGTACAAATGCTGGATCAGTGAAAGTTGAC
CCCGCTTTCATGTCTCTACTGGAGATTCCAAGTGACAGTGAGGAGAGTGCAATTAAGAGTGGATCCTCAATCTCACAGAG
TCTGCAGGGACTAAAGCAAGAACCAGCAGCAATGGCCCAAATGCAGGGA

Alignment

ORF - retro_ptro_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 72.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVDMDKLINNLEVQLNSEGGSMQVFKQVTASVRNRDPPEIEY-RSNMTSPTLLDANPMENPALFNDIKIE
          MVDMD.LINNLEVQLNSEGGSMQ.FK..T......DPPEIE..R.N.TSP.LLDANPMENPALFNDIK.E
Retrocopy MVDMDQLINNLEVQLNSEGGSMQIFKPITGPTQSTDPPEIEA<RNNVTSPPLLDANPMENPALFNDIKFE

Parental  P-PEELLASDFSLPQVEPVDLSFHKPKAPLQPASMLQAPIRPPKPQSSPQTLVVSTSTSDMSTSANIPTV
          P.PEELLASDFSL..VEPVD.S.HKPKAPL.P.SM.......P.....PQ.....T.....STSANIPT.
Retrocopy P<PEELLASDFSLSPVEPVDFSSHKPKAPLHPVSM----LQAPGHPAKPQS-APETLVVFTSTSANIPTI

Parental  LTPGSVLTSSQSTGSQQILHVIHTIPSVSLPNKMGGLKTIPVVVQSLPMVYTTLPADGGPAAITVPLIGG
          LT.GSVLT.SQ.TG..QILHVIH.IPSV.LP.KM..L..IPVVVQSLPMVYTTLPA..GPA..TVPLIGG
Retrocopy LTTGSVLTPSQGTGG*QILHVIHSIPSVCLPSKMDYLNAIPVVVQSLPMVYTTLPANEGPAPNTVPLIGG

Parental  DGKNAGSVKVDPTSMSPLEIPSDSEESTIESGSSALQSLQGLQQEPAAMAQMQG
          DG.NAGSVKVDP..MS.LEIPSDSEES.I.SGSS..QSLQGL.QEPAAMAQMQG
Retrocopy DGTNAGSVKVDPAFMSLLEIPSDSEESAIKSGSSISQSLQGLKQEPAAMAQMQG

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	4.49 RPM
SRP007412_cerebellum	0.04 RPM	10.86 RPM
SRP007412_heart	0.00 RPM	2.51 RPM
SRP007412_kidney	0.00 RPM	21.76 RPM
SRP007412_liver	0.00 RPM	1.80 RPM
SRP007412_testis	0.00 RPM	4.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1104 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000014678	1 retrocopy	retro_mmul_1561,
Pan troglodytes	ENSPTRG00000012850	1 retrocopy	retro_ptro_1948,
Pan troglodytes	ENSPTRG00000021957	1 retrocopy	retro_ptro_1104 ,
Pan troglodytes	ENSPTRG00000039565	2 retrocopies	retro_ptro_111, retro_ptro_2968,