RetrogeneDB ID: retro_ptro_1718

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:178755082..178755653(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC2
• Ensembl ID: ENSPTRG00000014852
• Aliases: None
• Description: leucine rich repeat containing 2 [Source:HGNC Symbol;Acc:14676]

Sequence

>retro_ptro_1718
AGTGGCTTCATAGACATTCATAGCATGCAGCTTCTGGAAAAGATAGAAAGGAAAGCTCTCACAAGGCAGAGTTCACTTCC
CAAGGACAGAGGCAAATGGAGCAGTGTGTTTGTGTTTGGACTTTCTGGGGAGCACTGGACGGAGCTGCCAGATTTGTTAA
AGGAGCAGACGCACCTGAGAGAATGGCATGTATGTGACACCCTGATTCAAATTACTCCTACATATATTGAGCTGTTTCAA
GCGATGAGAATTCAGGATCTGCCAAAGAAACAAATCTCACATTTTCCAGCTAAACTCAGTTGTTTGAAGAACCTGAAATA
ACTCAATGTGAGTTTCAACTATCTGAAGAGCATTCCTCCAGAGCTGGGAGATTGTGAAATCTAGAGGGACTGGATTGTTC
TGGAAATCTGGAATTCACAGAGATGCCTTTTGAATTAAGTAATTGGAAGCCAGTTGCATTCAAAGATATATCAGCAAACA
AGTTTTCCAGTGTCCCAGTTTGTGTCGTGAGGATGTCTATTTGCAGTCGTTGGATATCAGCAACAATAACCTGACTGCCT
TGCGGCAAGAT

Alignment

ORF - retro_ptro_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.76 %
• Parental protein coverage: 51.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGFIDT-SVRLLDKIERNTLTRQSSLPKDRGKRSSAFVFELSGEHWTELPDSLKEQTHLREWHISNTLIQ
          .GFID..S..LL.KIER..LTRQSSLPKDRGK.SS.FVF.LSGEHWTELPD.LKEQTHLREWH...TLIQ
Retrocopy SGFIDIHSMQLLEKIERKALTRQSSLPKDRGKWSSVFVFGLSGEHWTELPDLLKEQTHLREWHVCDTLIQ

Parental  IIPTYIQLFQAMRILDLPKNQISHLPAEIGCLKNLKELNVSFNYLKSIPPELGDCE-NLERLDCSGNLEL
          I.PTYI.LFQAMRI.DLPK.QISH.PA...CLKNLK.LNVSFNYLKSIPPELGDCE.NLE.LDCSGNLE.
Retrocopy ITPTYIELFQAMRIQDLPKKQISHFPAKLSCLKNLK*LNVSFNYLKSIPPELGDCE<NLEGLDCSGNLEF

Parental  MELPFELSNLKQVTFVDISANKFSSVPICVLRMS-NLQWLDISSNNLTDLPQD
          .E.PFELSN.K.V.F.DISANKFSSVP.CV.RMS..LQ.LDIS.NNLT.L.QD
Retrocopy TEMPFELSNWKPVAFKDISANKFSSVPVCVVRMS<YLQSLDISNNNLTALRQD

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	2.29 RPM
SRP007412_cerebellum	0.00 RPM	2.65 RPM
SRP007412_heart	0.00 RPM	49.37 RPM
SRP007412_kidney	0.00 RPM	2.72 RPM
SRP007412_liver	0.00 RPM	2.26 RPM
SRP007412_testis	0.00 RPM	0.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1718 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1718 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2346
Gorilla gorilla	retro_ggor_1782
Pongo abelii	retro_pabe_2124

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002149	1 retrocopy	retro_cjac_2714,
Homo sapiens	ENSG00000163827	1 retrocopy	retro_hsap_2346,
Gorilla gorilla	ENSGGOG00000004427	1 retrocopy	retro_ggor_1782,
Pongo abelii	ENSPPYG00000013932	1 retrocopy	retro_pabe_2124,
Pan troglodytes	ENSPTRG00000014852	1 retrocopy	retro_ptro_1718 ,