RetrogeneDB ID: retro_ptro_1685

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:246815738..246816311(+)
• Located in intron of: ENSPTRG00000013123

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD2
• Ensembl ID: ENSPTRG00000009629
• Aliases: None
• Description: None

Sequence

>retro_ptro_1685
GGTAGCTTGTCCAAATGGCTCTGGCTCAACATTGGTGGCACCTACTTTCTCACCACCCAGCAGATGCTGTGCCAGGACCT
GAAATACTTCCTGTACTCCTTGTATCAGGCTAACCCCGACAAGGATGCAACTGTTGCCTATTTAATGGACAGAGACCCCA
CCTATTTTGGGCCTGTGCTGAACTACCTGAGACGTGGCAAGCTGGTGATTAACAAAGACCTTGTGGAGGAAGGAGTGTTG
GAAAAAGCAGAATTTTACAGTATCACTTCATTAATCAAACTTGTAAAGGACAAAATTAGAGAACAAGAGAGCAAAACATC
ACAGGTGCCCATGAAGCATGTGTACCACGTGCTTCAGTGTCAGGAGGAGGAACTCACACAGGTGGTGTCCACCATGTCCG
ACAGCTGGAAGTTTGAACAACTGGTCAGCAGTGGCTCTTCTTACAACTATGGGAATGAAGATCAGGCCAAGTTCCTCTAT
GTGGTGTCCAAGGAACTTCACAACACCCCATACAGTATGGCCAGTGAACCCAGCAAGAAGACCAAGATTTTGCAAGAACC
AGGTTCCAGGATG

Alignment

ORF - retro_ptro_1685 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 74.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGAARWVRLNVGGTYFVTTRQTLGREPKSFLCRLCCQEDPELDSDKDETGAYLIDRDPTYFGPILNYLRH
          G....W..LN.GGTYF.TT.Q.L....K.FL..L..Q..P.....KD.T.AYL.DRDPTYFGP.LNYLR.
Retrocopy GSLSKWLWLNIGGTYFLTTQQMLCQDLKYFLYSL-YQANPD----KDATVAYLMDRDPTYFGPVLNYLRR

Parental  GKLIITKELAEEGVLEEAEFYNIASLVRLVKERIRDNENRTSQGPVKHVYRVLQCQEEELTQMVSTMSDG
          GKL.I.K.L.EEGVLE.AEFY.I.SL..LVK..IR..E..TSQ.P.KHVY.VLQCQEEELTQ.VSTMSD.
Retrocopy GKLVINKDLVEEGVLEKAEFYSITSLIKLVKDKIREQESKTSQVPMKHVYHVLQCQEEELTQVVSTMSDS

Parental  WKFEQLISIGSSYNYGNEDQAEFLCVVSRELNNSTNGIVIEPSEKAKILQERGSRM
          WKFEQL.S.GSSYNYGNEDQA.FL.VVS.EL.N.......EPS.K.KILQE.GSRM
Retrocopy WKFEQLVSSGSSYNYGNEDQAKFLYVVSKELHNTPYSMASEPSKKTKILQEPGSRM

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	0.27 RPM	23.56 RPM
SRP007412_cerebellum	0.43 RPM	111.92 RPM
SRP007412_heart	0.03 RPM	10.35 RPM
SRP007412_kidney	0.24 RPM	14.10 RPM
SRP007412_liver	0.13 RPM	5.04 RPM
SRP007412_testis	0.00 RPM	25.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1685 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1685 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2224
Gorilla gorilla	retro_ggor_1752
Pongo abelii	retro_pabe_2093

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021231	1 retrocopy	retro_btau_927,
Callithrix jacchus	ENSCJAG00000014605	1 retrocopy	retro_cjac_2781,
Echinops telfairi	ENSETEG00000013965	1 retrocopy	retro_etel_643,
Pongo abelii	ENSPPYG00000008616	1 retrocopy	retro_pabe_2093,
Pan troglodytes	ENSPTRG00000009629	1 retrocopy	retro_ptro_1685 ,
Pan troglodytes	ENSPTRG00000020092	3 retrocopies	retro_ptro_1225, retro_ptro_2166, retro_ptro_2825,