RetrogeneDB ID: retro_ptro_689

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:45170769..45171123(+)
• Located in intron of: ENSPTRG00000004847

Retrocopy information

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

Parental gene information

• Parental gene symbol: IQCF1
• Ensembl ID: ENSPTRG00000014977
• Aliases: None
• Description: IQ motif containing F1 [Source:HGNC Symbol;Acc:28607]

Sequence

>retro_ptro_689
AAGAAGCAGCCTAAAAAAATGAATAAACCCACACACACAAAAGATGAGCCTCAGCAGAAGGACATGATGGCCCATTTTTC
TTCGGGACCATTAACCTCAAAGTTGAAGGCAGAGGCCAAAACTCTGGCTCTGGTTAAGACACAAACAGTGGCTAATGCCA
ATGAGAAATTTGGAAAACCCCCAGAAAACCAAAAGAAGCTCTCTGACAAAGATATGGCAGTCATCAAGATCCAAGCCTGG
TGTTGGGGCACCCTGGTACATCAGGCACTGTGGCACACAGCCCTCAGCACCTGGATCATTCAGTGCTGATGGTGGCTGAT
GCTGTCCAGGATTCTGGAGATGAGGCAGTGGGCA

Alignment

ORF - retro_ptro_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.02 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKQPKKTKEPSK-EDEPQQKETPTHLSLG---AESKAEAKTPVLVETQTVDNANEKSEKPPENQKKLSDK
          .KQPKK...P....DEPQQK....H.S.G......KAEAKT..LV.TQTV.NANEK..KPPENQKKLSDK
Retrocopy KKQPKKMNKPTHTKDEPQQKDMMAHFSSGPLTSKLKAEAKTLALVKTQTVANANEKFGKPPENQKKLSDK

Parental  DTVATKIQAWWRGTLVRRALLHAALSACIIQCWWRLILSKILKKRRRA
          D....KIQAW..GTLV..AL.H.ALS..IIQC.W.L.LS.IL..R..A
Retrocopy DMAVIKIQAWCWGTLVHQALWHTALSTWIIQC*WWLMLSRILEMRQWA

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	0.14 RPM
SRP007412_cerebellum	0.00 RPM	0.14 RPM
SRP007412_heart	0.03 RPM	0.03 RPM
SRP007412_kidney	0.03 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	55.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_689 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_689 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1109
Macaca mulatta	retro_mmul_860

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000173389	1 retrocopy	retro_hsap_1109,
Gorilla gorilla	ENSGGOG00000012462	1 retrocopy	retro_ggor_867,
Macaca mulatta	ENSMMUG00000004352	1 retrocopy	retro_mmul_860,
Pan troglodytes	ENSPTRG00000014977	1 retrocopy	retro_ptro_689 ,