RetrogeneDB ID: retro_pabe_2124

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:64392091..64392851(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC2
• Ensembl ID: ENSPPYG00000013932
• Aliases: None
• Description: leucine-rich repeat-containing protein 2 [Source:RefSeq peptide;Acc:NP_001125602]

Sequence

>retro_pabe_2124
AATGGCTTCACAGACATTCATAGCATGCGGCTTCTGGAAAAGACAGAAAGGAAGGCTCTCACAAGGCAGAGTTCACTTCC
CAAGGACAGAGGCAAATGGAGCAGTGCGTTTGTGTTTGGACTTTCTGGGGAGCACTGGACGGAGCTGCCAGATTTGTTGA
AGGAGTAGACGCACCTGAGAGAATGGCATGTGTGCGACACCCTGATTCAAATCACTCCTACATATATTGAGCTGTTTCAA
GCGATGAGAATTCAGGATCTGCCAAAGAAACAAATCTCACATTTTCCAGCTAAAATCAGTTGTTTGAAGAACCTGAAATA
ACTCAATGTGACTTTCAACTATCTGAAGAGCATTCCTCCAGAGCTGGGAGATTGTGAAATCTAGAGGGACTGGATTGTTC
TGGAAATCTGGAATTCACAGAGCTGCCTTTTGAATTAAGTAATCGGAAGCCAGTTGCATTCGTAGATATCTCAGCAAACA
AGTTTTCCAGTGTCCCAATCTGTGTCCTGAGGATGTCTATTTGCAGTGGTTGGATATCAGCAACAATAACCTGACTGCCT
TGCAGCAAGATAGAGACAGGCTGGAAGAGCTGCAGGGCTTTCTCTTGTATAAAAGCAAGTTGACCTACCTTCTTTACCCC
ATGCTTAACCTGAAGAAGCACACCTTGTTAGTCGTCAATGGGGACCACTTGGTGGAGCTTTCAACTGCACTTTGTGACTC
CTCCACACCTTTAAAATTTGTAAGCCTTATGAACAATCCC

Alignment

ORF - retro_pabe_2124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.64 %
• Parental protein coverage: 68.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGFIDT-SVRLLDKIERNTFTRQSSLPKDRGKRSSAFVFELSGEHWTELPDSLKEQTHLREWHISNTLIQ
          NGF.D..S.RLL.K.ER...TRQSSLPKDRGK.SSAFVF.LSGEHWTELPD.LKE.THLREWH...TLIQ
Retrocopy NGFTDIHSMRLLEKTERKALTRQSSLPKDRGKWSSAFVFGLSGEHWTELPDLLKE*THLREWHVCDTLIQ

Parental  IIPTYIELFQAMRILDLPKNQISHLPAEIGCLKNLKELNVSFNHLKSIPPELGDCE-NLERLDCSGNLEL
          I.PTYIELFQAMRI.DLPK.QISH.PA.I.CLKNLK.LNV.FN.LKSIPPELGDCE.NLE.LDCSGNLE.
Retrocopy ITPTYIELFQAMRIQDLPKKQISHFPAKISCLKNLK*LNVTFNYLKSIPPELGDCE<NLEGLDCSGNLEF

Parental  MELPFELSNLKQVTFVDISANKFSSVPICVLRMS-NLQWLDISNNNLTDLPQDIDRLEELQSFLLYKNKL
          .ELPFELSN.K.V.FVDISANKFSSVPICVLRMS..LQWLDISNNNLT.L.QD.DRLEELQ.FLLYK.KL
Retrocopy TELPFELSNRKPVAFVDISANKFSSVPICVLRMS<YLQWLDISNNNLTALQQDRDRLEELQGFLLYKSKL

Parental  TYLPYCMLNMKKLILLVVSGDHLVELPTALCDSSTPLKFVSLMDNP
          TYL.Y.MLN.KK..LLVV.GDHLVEL.TALCDSSTPLKFVSLM.NP
Retrocopy TYLLYPMLNLKKHTLLVVNGDHLVELSTALCDSSTPLKFVSLMNNP

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	0.44 RPM
SRP007412_cerebellum	0.00 RPM	0.73 RPM
SRP007412_heart	0.00 RPM	69.90 RPM
SRP007412_kidney	0.00 RPM	1.06 RPM
SRP007412_liver	0.00 RPM	0.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2124 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2124 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2346
Pan troglodytes	retro_ptro_1718
Gorilla gorilla	retro_ggor_1782

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 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	ENSPPYG00000002651	1 retrocopy	retro_pabe_252,
Pongo abelii	ENSPPYG00000013932	1 retrocopy	retro_pabe_2124 ,
Pan troglodytes	ENSPTRG00000014852	1 retrocopy	retro_ptro_1718,