RetrogeneDB ID: retro_ptro_2443

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:74257191..74257680(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLRC3
• Ensembl ID: ENSPTRG00000029781
• Aliases: KLRC3, NKG2E
• Description: Pan troglodytes killer cell lectin-like receptor subfamily C, member 3 (KLRC3), mRNA. [Source:RefSeq mRNA;Acc:NM_001009017]

Sequence

>retro_ptro_2443
GGTTTACTGCCACCTCCAGAGAAGCTCACTGCTGAGGTCCTGGGAATCATTTGCATTGTCCTGATGTCTGCTGTGTGAAA
AACGATAGTTCTTATTCCTTTCCTGGAGCAGAACAATTCTTCCCCAAATACAAGAACCCAGAAAGCACGTCCTTGTGGCC
ATTGTCCTGAGGAGTGGATTACATATTCCAACAGTTGTTTTTACATTGGTAAGGAAAGAAGAACTTGGGAAGAGAGTTTG
CAGGCCTGTGCTTCAAAGAACTCTTCTAGTCTGCTTTCTATAGATAATGAAGAAGAAATGAAATTTCTGGCCAGCATTTT
ACCTTCCTCATGGATTGGTGTGTTTCGTAACAGCAGTCATCATCCATGGGTGACAATAAATGGTTTGGCTTTCAAACATG
AGATAAAAGACTCAGATCATGCTGAACGTAACTGTGCAATGCTACATGTACGTGGACTTATATCAGACCAGTGTGGATCT
TCAAGAATC

Alignment

ORF - retro_ptro_2443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.32 %
• Parental protein coverage: 67.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLLPPPEKLTAKMLGIICIVLMSAVLKTIVLIPFLEQNNSSPNTRTQKARPCGHCPEEWITYSNSCYYIG
          GLLPPPEKLTA..LGIICIVLMSAV.KTIVLIPFLEQNNSSPNTRTQKARPCGHCPEEWITYSNSC.YIG
Retrocopy GLLPPPEKLTAEVLGIICIVLMSAV*KTIVLIPFLEQNNSSPNTRTQKARPCGHCPEEWITYSNSCFYIG

Parental  KERRTWEESLQACASKNSSSLLSIDNEEEIKFLASILPSSWIGVFCNSSHHPWVTINGLAFKHEIKDSDH
          KERRTWEESLQACASKNSSSLLSIDNEEE.KFLASILPSSWIGVF.NSSHHPWVTINGLAFKHEIKDSDH
Retrocopy KERRTWEESLQACASKNSSSLLSIDNEEEMKFLASILPSSWIGVFRNSSHHPWVTINGLAFKHEIKDSDH

Parental  AERNCAMLHVRGLISDQCGSSRI
          AERNCAMLHVRGLISDQCGSSRI
Retrocopy AERNCAMLHVRGLISDQCGSSRI

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	0.07 RPM	0.21 RPM
SRP007412_cerebellum	0.07 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.03 RPM
SRP007412_liver	0.00 RPM	0.07 RPM
SRP007412_testis	0.00 RPM	0.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2443 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2443 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000029781	1 retrocopy	retro_ptro_2443 ,
Tarsius syrichta	ENSTSYG00000019371	1 retrocopy	retro_tsyr_926,