RetrogeneDB ID: retro_ptro_3254

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:101886552..101887510(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKCI
• Ensembl ID: ENSPTRG00000015615
• Aliases: None
• Description: None

Sequence

>retro_ptro_3254
CGTATTTATGCAATGAAAGTTGTGAAAAAAGAGCTTGTTAATGATGATGAGGATATTGATTGGGTGCAGACAGAGAAACA
TGTGTTTGAGCAGGCATCCAATCATCCTTTCCTTGTTGGGCTGCAGTCTTGCTTTCAGACAGAAAGCAGATTGTTCTTTG
TTATAGAGTATGTAAATGGAGGAGACCTAATGTTTCATATGCAGCGACAAAGAAAACTTCCTGAAGAACATGCCAGATTT
TACTCTGCAGAAATCAGTCTAGCATTCAATTATCTTCATGAGTGAGGGATAATTTATAGAGATTTGAAACTGGACAATGT
ATTACTAGACTCTGAAGGCCACATTAAACTCACTGACTACGGCATGTGTTAAGGAAGGATTACGGCCAGGAGATACAACC
AGCACTTTCTGTGGTACTCCTAATTACATTGCTCCTGAAATTTTAAGAGGAGGAGATTATGGTTTCAGTGTTGACTGGTG
GGCTCTTGGAGTGCTAATGTTTGAGACGATGGCAGGAAGGACTCCACTTGATACTGTTGGGAGCTCCGATAACCCTGACC
AGAACACAGAGGATTCTCTCTTCCAAGTTATTGTGGAAAAACAAATTCACATACCACGTTCTCTGTCTGTAAAAGCTGAA
AGTGTTCTGAAGAGTTTTCTTAACAAGGACCCTAAGAAAAGACTGGGTTGTCATCCTCAAACAGGATTTGCTGATATTCA
GGGACACCCGTTCTTCCAAAATGTTGATTGGGATATGATGGAGCAAAAACAGGTGGTATCTCCCTTTAAACCAAATATTT
CTGGGGAATTTGGTTTGGACAACTTTGATTCTCAGTTTACTAATGAACCTGTCCAGCTCACTCCAGATGTCGATGACATT
GTGAGAAAGATTGATCAGTCTGAATTTGAAGGTTTTGAGTATATCAATCCTCTTTTGATGTCTGCAGAAGAATGTGTC

Alignment

ORF - retro_ptro_3254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.69 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RIYAMKVVKKELVNDDEDIDWVQTEKHVFEQASNHPFLVGLHSCFQTESRLFFVIEYVNGGDLMFHMQRQ
          RIYAMKVVKKELVNDDEDIDWVQTEKHVFEQASNHPFLVGL.SCFQTESRLFFVIEYVNGGDLMFHMQRQ
Retrocopy RIYAMKVVKKELVNDDEDIDWVQTEKHVFEQASNHPFLVGLQSCFQTESRLFFVIEYVNGGDLMFHMQRQ

Parental  RKLPEEHARFYSAEISLALNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC-KEGLRPGDTTSTFCGT
          RKLPEEHARFYSAEISLA.NYLHE.GIIYRDLKLDNVLLDSEGHIKLTDYGMC.KEGLRPGDTTSTFCGT
Retrocopy RKLPEEHARFYSAEISLAFNYLHE*GIIYRDLKLDNVLLDSEGHIKLTDYGMC>KEGLRPGDTTSTFCGT

Parental  PNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLFQVILEKQIRIPRSLS
          PNYIAPEILRG.DYGFSVDWWALGVLMFE.MAGR.P.D.VGSSDNPDQNTED.LFQVI.EKQI.IPRSLS
Retrocopy PNYIAPEILRGGDYGFSVDWWALGVLMFETMAGRTPLDTVGSSDNPDQNTEDSLFQVIVEKQIHIPRSLS

Parental  VKAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKPNISGEFGLDNFDSQF
          VKA.SVLKSFLNKDPK.RLGCHPQTGFADIQGHPFF.NVDWDMMEQKQVV.PFKPNISGEFGLDNFDSQF
Retrocopy VKAESVLKSFLNKDPKKRLGCHPQTGFADIQGHPFFQNVDWDMMEQKQVVSPFKPNISGEFGLDNFDSQF

Parental  TNEPVQLTPDDDDIVRKIDQSEFEGFEYINPLLMSAEECV
          TNEPVQLTPD.DDIVRKIDQSEFEGFEYINPLLMSAEECV
Retrocopy TNEPVQLTPDVDDIVRKIDQSEFEGFEYINPLLMSAEECV

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	0.02 RPM	10.44 RPM
SRP007412_cerebellum	0.00 RPM	14.27 RPM
SRP007412_heart	0.00 RPM	5.42 RPM
SRP007412_kidney	0.03 RPM	12.13 RPM
SRP007412_liver	0.00 RPM	2.78 RPM
SRP007412_testis	0.11 RPM	15.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3254 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3254 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4884
Pongo abelii	retro_pabe_3798

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015212	1 retrocopy	retro_cpor_656,
Homo sapiens	ENSG00000163558	1 retrocopy	retro_hsap_4884,
Pongo abelii	ENSPPYG00000014289	1 retrocopy	retro_pabe_3798,
Pan troglodytes	ENSPTRG00000015615	1 retrocopy	retro_ptro_3254 ,