RetrogeneDB ID: retro_ptro_2166

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:77642979..77644146(+)
• Located in intron of: ENSPTRG00000016806

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD9
• Ensembl ID: ENSPTRG00000020092
• Aliases: None
• Description: None

Sequence

>retro_ptro_2166
ATGAGGCGGGTGACCCTATTCCTGAACAGCAGCCCCAAGAATGGAAAGGTGGTTGCTGTATATGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGCAGTAAACTCAGCATAAAAGCCACCAGTGTGTATAATGAGAAAGGTGGACTGACTGATGATATTG
CTTTGATCAGGGATGATGATGTTTTACTTGTGTGTGAGGGAGAGCCATTTATTGATCTTCAGACAGATTCTAAGCCTCCT
GAAGGATTGTTAGGATTCCACACAGAATGGCTAACATTAAATGCTGCAGGGAGGTACTTTACAACTACACGGAGCACTTT
AGCGAATAAAGAACCTGACAGTATGCTGGCCCACATGCTTAAGAACAGAGGTGTCTGGGGAAATAAGCAAGATCATAGAG
GAGCCTTCTTAATTGACCAAAGTCCTGAGTACTTTGAACCCACTTTGAACTACTTGTGTCATGGACAGCTCATTGTAAAT
GATGGCATTAATTTATTGGGTGTGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCACTGATTGAACACCTAGAAGTGGC
AATAAAGAATTCTCAATCACCAGAGGATCATTCACCAATATCTCGAAAGGAATTTGTCCGATTTTTGGTAGCAACTCCAA
CCAAGTCAGAACTGTGATACCAGAGTTTGAACTTCAGTGGTGCTGATGTTTCTCGTTAGGACCTTCAATACATTAACTTC
AAAATGGCCAATTTAAGCCGCTGCAATCTTGCACATGCAAATCTTTACTGTGCAAATCTTGAATGAGGTGATCTCTCTGG
ATCAGTGCTTGACTGTGCAAATCTCCAGGGAGTCAAGATGCTCTGTTCTAATGCAGAAGGAGCATCCCTGAAACTGTGTA
ATTTTGAGGATCTTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAATCTGAAAGGTGTGGATATGGAAGGAAGTCAGATG
ACAGGAATTAACCTGAGAGTGGCTACCTTAAAAAATGCAAAGTTGAAGAATTGTAACCTCAGAGGAGCAACTCTGGCAGG
AACCAATTTAGAGAACTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACTTGAGAGGGTCCAACGTGAAGGGAGCTA
CATTTGAAGAGATGCTGACACCACTATACATGTCGCAAAATGTCAGA

Alignment

ORF - retro_ptro_2166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEPF
          MRRVTLFLN.SPKNGKVVAVYGTLSDLLSVASSKL.IKATSVYN.KGGL.DDIALIRDDDVL.VCEGEPF
Retrocopy MRRVTLFLNSSPKNGKVVAVYGTLSDLLSVASSKLSIKATSVYNEKGGLTDDIALIRDDDVLLVCEGEPF

Parental  IDPQTDSKPPEGLSGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAFLIDR
          ID.QTDSKPPEGL.GFHT.WLTLN..GRYFTTTRSTL.NKEPDSMLAHM.K..GVWGNKQDHRGAFLID.
Retrocopy IDLQTDSKPPEGLLGFHTEWLTLNAAGRYFTTTRSTLANKEPDSMLAHMLKNRGVWGNKQDHRGAFLIDQ

Parental  SPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFLL
          SPEYFEP.LNYL.HGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQ.PEDHSPISRKEFVRFL.
Retrocopy SPEYFEPTLNYLCHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQSPEDHSPISRKEFVRFLV

Parental  ATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGVKM
          ATPTKSEL..Q.LNFSGAD.SR.DL.YINFKMANLSRCNLAHANL.CANLE..DLSGSVLDCANLQGVKM
Retrocopy ATPTKSEL*YQSLNFSGADVSR*DLQYINFKMANLSRCNLAHANLYCANLE*GDLSGSVLDCANLQGVKM

Parental  LCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTDL
          LCSNAEGASLKLCNFED.SGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGT.L
Retrocopy LCSNAEGASLKLCNFEDLSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGTNL

Parental  ENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          ENCDLSGCDLQEANLRGSNVKGA.FEEMLTPL.MSQ.VR
Retrocopy ENCDLSGCDLQEANLRGSNVKGATFEEMLTPLYMSQNVR

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	4.67 RPM
SRP007412_cerebellum	0.04 RPM	4.95 RPM
SRP007412_heart	0.00 RPM	16.58 RPM
SRP007412_kidney	0.00 RPM	5.75 RPM
SRP007412_liver	0.00 RPM	2.39 RPM
SRP007412_testis	0.32 RPM	8.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2166 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2166 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3305
Gorilla gorilla	retro_ggor_1309
Pongo abelii	retro_pabe_2725

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Homo sapiens	ENSG00000104756	4 retrocopies	retro_hsap_1730, retro_hsap_3305, retro_hsap_4037, retro_hsap_4156,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Pan troglodytes	ENSPTRG00000009629	1 retrocopy	retro_ptro_1685,
Pan troglodytes	ENSPTRG00000020092	3 retrocopies	retro_ptro_1225, retro_ptro_2166 , retro_ptro_2825,