RetrogeneDB ID: retro_ptro_1225

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:35875288..35876452(-)
• Located in intron of: ENSPTRG00000008878

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_1225
ATGAGGTGGGTGGCCCTGTTCCTGAACGGCAGCCCCAAGAACGGAAAGGTGGTTGCTGTATGTGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGTGGTAAACTTGGCATAAAAGCCACCAGTGTGTATAATGGCAAAGGTGGACTGATTGATGATATTG
CTTTGATCAGGGATGATGATGTTTTGTTTGTGTGTGAAGGAAAGCCATTTATTGATCCTGACAGATTCTAAACCACCTGA
GGGATTGTCAGGATTCCACATAGACTGGCTAACATTAAATGCTGGAGGGCGGTACTTTACAACCACACAGAGCACTTTAG
TGAATAAAGAACCTGATAGTATGCTGGCCCACATGTTTAAGGACAAAGATGTCTGGGAAATAAGCAAGATCACAGAGGAG
CTTTCTTAATTGACCGAAGTCCTGAGTACTTTGAACCCATTTTGAACTACTTGCATCATGGACAGCTTATTGTACATGAT
GGCTTTAATTTATTGGATATGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCATTGATTGAACACCTAGAAATGGCAAT
AAAGAATTCTAAACCACCGGAGGATCATTCACCAATATCCTGAAAGGAATTTGTCTGATTTTTGCTGGCAACTTCAATCA
AGTCAGAACTGCGATGCCAAGGTTTGAACTTCAGTGGTGCTGATCTTTCTCATTTGGACCTTTGAAACATTAACTTCAAA
ATGGCCAGTTTAAGCCACTGCAGTCTTGCACATGCAAATCTTTGCTGTGCAAATCTTAAACAAGCTGATCTCTCTGGATC
AGTGCTTGACTGTGCAAATCTCCAGGGAGTCAAGACACTCTGTTCTAATGTAGAAGGAGCATCCCTGAAACTGTGTAATT
TTGAGGATCCTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAACCTGAAAGGTGTGGATATGGAAGGAAGTCAGATAACA
GGAATTAACCTGAGAGTGACTACCTTAAAAAATGCAAAGTTGAAGAACTGTAACCTCAGAGGAGCAACTCTAGCAGGAAC
TGATTTAGAGAACTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACCTGAGAGGGTCCAACATGAAGGGAGCTAGAT
TTGAAGAGATGCTAACACCACTACACATGTCACAAAGTGTTAGA

Alignment

ORF - retro_ptro_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDD-VLFVCEGEP
          MR.V.LFLNGSPKNGKVVAV.GTLSDLLSVAS.KLGIKATSVYNGKGGLIDDIALIR.DD.....C..E.
Retrocopy MRWVALFLNGSPKNGKVVAVCGTLSDLLSVASGKLGIKATSVYNGKGGLIDDIALIR-DD>MFCLCVKES

Parental  FIDPQTDSKPPEGLSGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVW-GNKQDHRGAFLI
          .....TDSKPPEGLSGFH.DWLTLN.GGRYFTTT.STLVNKEPDSMLAHMFKDK.VW.GNKQDHRGAFLI
Retrocopy HLLILTDSKPPEGLSGFHIDWLTLNAGGRYFTTTQSTLVNKEPDSMLAHMFKDKDVW<GNKQDHRGAFLI

Parental  DRSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRF
          DRSPEYFEPILNYL.HGQLIV.DG.NLL..LEEARFFGIDSLIEHLE.AIKNS.PPEDHSPIS.KEFV.F
Retrocopy DRSPEYFEPILNYLHHGQLIVHDGFNLLDMLEEARFFGIDSLIEHLEMAIKNSKPPEDHSPIS*KEFV*F

Parental  LLATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGV
          LLAT..KSELRCQGLNFSGADLS.LDL..INFKMA.LS.C.LAHANLCCANL..ADLSGSVLDCANLQGV
Retrocopy LLATSIKSELRCQGLNFSGADLSHLDL*NINFKMASLSHCSLAHANLCCANLKQADLSGSVLDCANLQGV

Parental  KMLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGT
          K.LCSN.EGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQ.TGINLRV.TLKNAKLKNCNLRGATLAGT
Retrocopy KTLCSNVEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQITGINLRVTTLKNAKLKNCNLRGATLAGT

Parental  DLENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          DLENCDLSGCDLQEANLRGSN.KGA.FEEMLTPLHMSQSVR
Retrocopy DLENCDLSGCDLQEANLRGSNMKGARFEEMLTPLHMSQSVR

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	0.34 RPM	4.67 RPM
SRP007412_cerebellum	0.18 RPM	4.95 RPM
SRP007412_heart	0.09 RPM	16.58 RPM
SRP007412_kidney	0.00 RPM	5.75 RPM
SRP007412_liver	0.00 RPM	2.39 RPM
SRP007412_testis	0.00 RPM	8.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1225 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1225 has 0 orthologous retrocopies within eutheria group .

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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,