RetrogeneDB ID: retro_ptro_2825

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:37977143..37978308(+)
• Located in intron of: None

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_2825
ATGAGGCGGGTGACCCTGTTCCTGAACGGCAGCCCCAAGAATGGAAAGGTGGTTGCTGATATGGAACTTTATCTGATTTG
CTGTCTGGGGCCAGCAGTAAACTCGGCATAAAAGCCACCAGTGTGTATAATGGGAAAGGTGGACTGAATGATGATATTGT
TTTGATCAGGGATGATGATGTTTTATTTGTGTGTGAGGGAGAGCCATTTATTGATCCTCAGACAGATTCTAAGCCTCCTG
AAGGATTGCTAGGATTCCACACAGACTGGCTAACATTACATGTTGGAGGGCAGTACTTTACAACTACCTGGAGCACTTTA
GTGAATAAAGAACCTGACATTATGCTGGCCCACATGTTTAAGGACAAAGGTGTCTGGGGAGATAAGCAAGATCATAGAGG
AGCTTTCTTAATTGACCAAAGTCCTGGGTACTTTGAACCCATTTTGAACTACTTGCGTCATGGACAGCTCATTGTAAATG
ATGGCATTGATTTATTGGGTGTGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCATTGATTGAACACCTAAAAGTGGCA
ATAAAGAATTCTCAACCACCAGAGGATCATTTACCAATATCCCGAAAGGAATTTGTCCGATGTTTGCTAGCAACTCCAAC
CAAGTCAGAAATGCGATGCCAGGGTTTGAACTTCAGTGGTGCTGAACTTTCTCATTTGGATCTTCGATACATTAACTTCA
AAATCACCAATTTAAACTGCTGCAATCTTGCACATGCAAATCTTTGCTGTGCAAATCTTGAATGAGCTGATCTCTCTGGA
TCAGTGCTTGACTGTGCAAATCTCCAGGGAGTCAAATGCTCTGTTCTAATGCAGAAGGAGCATCTCTGAAACGGTGTAAT
TTTGAGGATCCTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAATCTGAAAGGTGTGGATATGGAAGGAAGTCAGATGAC
AGGAATTAACCTGAGAGTGGCTACCTTAAAAAATGCAAAGTTGAAGAACTGTAGCCTCAGAGGAGCAACTCTGACAGGAA
CTGATTTAGAGAACTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACCTGAGAGGGTCCAACGTGAGGGGAGCTAGA
TTTGAAGAGATGCTGACACCACTACACGTGTCGCAAAGTGTCAGA

Alignment

ORF - retro_ptro_2825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAV-YGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEP
          MRRVTLFLNGSPKNGKVVA..YGTLSDLLS.ASSKLGIKATSVYNGKGGL.DDI.LIRDDDVLFVCEGEP
Retrocopy MRRVTLFLNGSPKNGKVVAD<YGTLSDLLSGASSKLGIKATSVYNGKGGLNDDIVLIRDDDVLFVCEGEP

Parental  FIDPQTDSKPPEGLSGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAFLID
          FIDPQTDSKPPEGL.GFHTDWLTL.VGG.YFTTT.STLVNKEPD.MLAHMFKDKGVWG.KQDHRGAFLID
Retrocopy FIDPQTDSKPPEGLLGFHTDWLTLHVGGQYFTTTWSTLVNKEPDIMLAHMFKDKGVWGDKQDHRGAFLID

Parental  RSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRFL
          .SP.YFEPILNYLRHGQLIVNDGI.LLGVLEEARFFGIDSLIEHL.VAIKNSQPPEDH.PISRKEFVR.L
Retrocopy QSPGYFEPILNYLRHGQLIVNDGIDLLGVLEEARFFGIDSLIEHLKVAIKNSQPPEDHLPISRKEFVRCL

Parental  LATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGVK
          LATPTKSE.RCQGLNFSGA.LS.LDLRYINFK..NL..CNLAHANLCCANLE.ADLSGSVLDCANLQGVK
Retrocopy LATPTKSEMRCQGLNFSGAELSHLDLRYINFKITNLNCCNLAHANLCCANLE*ADLSGSVLDCANLQGVK

Parental  -MLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGT
          .MLCSNAEGASLK.CNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNC.LRGATL.GT
Retrocopy <MLCSNAEGASLKRCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCSLRGATLTGT

Parental  DLENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          DLENCDLSGCDLQEANLRGSNV.GA.FEEMLTPLH.SQSVR
Retrocopy DLENCDLSGCDLQEANLRGSNVRGARFEEMLTPLHVSQSVR

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	0.00 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	0.00 RPM	8.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2825 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2825 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4156
Gorilla gorilla	retro_ggor_2791

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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 ,