RetrogeneDB ID: retro_ptro_1136

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:30967080..30967523(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C20orf27
• Ensembl ID: ENSPTRG00000013204
• Aliases: None
• Description: chromosome 20 open reading frame 27 [Source:HGNC Symbol;Acc:15873]

Sequence

>retro_ptro_1136
TCCCAGAGACACGTCTGCTTTGATGAGAGGCTTCATGACTCGGTGGTCATGGCCACCCAGGACAGCGACAGCAGCTTTCT
GGTCAAGGTTGGCTTCCTGAAGATCCTGCGCAGGTATGAGATTACCTTCACTCTGCCCCCGCCCAGTGAGCAAGCACGTC
CGTGAGGCACCTGTTCCCAGCCTCTGCATGTCAAGCTCCTCAGCGTTGTTCCTGTCCCTGAAGGTTACAGTGTCAAGTGC
AAGTACTCAGCGCACAAAGAGGGTGTCCTCAAAGCCGCGATGCTGCCAGCCTGAGAAGGTGGCGCCGGCGCCTGTGTGAG
CGTGGCAGTGCAGGCTGGCGCCAGGGGCCGACACCACGGCGTGCCCACCTGCGGGACGGTGTCAAGGGCTCGGGCGCCGC
GCTGGAATACGACTCGCAGCACAGCCACTGGCACGGCTTTGAC

Alignment

ORF - retro_ptro_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 74.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHSHVHFDEKLHDSVVMVTQESDSSFLVKVGFLKILHRYEITFTLPPVHRLSKDVREAPVPSLHLKLLSV
          S..HV.FDE.LHDSVVM.TQ.SDSSFLVKVGFLKIL.RYEITFTLPP.............P.LH.KLLSV
Retrocopy SQRHVCFDERLHDSVVMATQDSDSSFLVKVGFLKILRRYEITFTLPPPSEQARP*GTCSQP-LHVKLLSV

Parental  VPIPEGYSVKCEYSAHKEGVLKEEILLACEGGTGTCVRVTVQARVMDRHHGTPM-LLDGVKCVGAELEYD
          VP.PEGYSVKC.YSAHKEGVLK...L.A.EGG.G.CV.V.VQA....RHHG.P..L.DGVK..GA.LEYD
Retrocopy VPVPEGYSVKCKYSAHKEGVLKAAMLPA*EGGAGACVSVAVQAGARGRHHGVPT<LRDGVKGSGAALEYD

Parental  SEHSDWHGFD
          S.HS.WHGFD
Retrocopy SQHSHWHGFD

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	0.29 RPM	27.88 RPM
SRP007412_cerebellum	0.25 RPM	20.61 RPM
SRP007412_heart	0.03 RPM	5.60 RPM
SRP007412_kidney	0.08 RPM	16.34 RPM
SRP007412_liver	0.03 RPM	17.55 RPM
SRP007412_testis	18.13 RPM	27.19 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1136 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1136 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1673

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021194	1 retrocopy	retro_cjac_3292,
Homo sapiens	ENSG00000101220	2 retrocopies	retro_hsap_1114, retro_hsap_1673,
Gorilla gorilla	ENSGGOG00000016987	1 retrocopy	retro_ggor_871,
Macaca mulatta	ENSMMUG00000022079	1 retrocopy	retro_mmul_1578,
Nomascus leucogenys	ENSNLEG00000007653	1 retrocopy	retro_nleu_194,
Pongo abelii	ENSPPYG00000010813	1 retrocopy	retro_pabe_923,
Pan troglodytes	ENSPTRG00000013204	2 retrocopies	retro_ptro_1136 , retro_ptro_685,