RetrogeneDB ID: retro_ptro_1961

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:197239828..197240821(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VEZF1
• Ensembl ID: ENSPTRG00000009442
• Aliases: None
• Description: vascular endothelial zinc finger 1 [Source:HGNC Symbol;Acc:12949]

Sequence

>retro_ptro_1961
GCTTCCCATCACCAACAGCAGGCAGCACAGAACAGCTTGCTGCCCCTCCTGAGCTCTGCCGTGGAGACCCCTGATCAGAA
ACCATTGCTTCCAATACCGATAACTCAGAAACCTCAGGGTGCACCAGAAACATTAAAGGATGCCATTGGGATTAAAAAAG
AAAAACCCAAAACTTCGTTTGTGTGCACTTACTGCAGTAAAGCTTTCAGGGACAGCTATCACCTGAGGCGCCATGAATCC
TGCCACACAGGGATCAAGGTGGTGTCCCGGCCAAAGAAAACCCCCACCACGGTGTTTCCCCTTATCTCTACCATCGCTGG
GGACAGCAGCCGAACTTCGTTGGTCTCGACCATTGCAGGCGTCTTGTCAACAGTCACTACATCTTCCTCGGGCACCAACC
CCAGTAGCAGTGCCAGCACCACAGCTCTGCCGGTGACTCAATCTGTCAAGAAACCCAGTAAGCCTGTCAAGAAGAACCAG
GCTTGTGAAATGTGTGGGAAGGCCTTCCGAGATGTGTACCATCTCAGTGGGCACAAGCTCTCCCATTCAGATGAGAAGCC
CTTCGAGTGTCCTATTTGTAATCAGCGCTTCAAGAGGAAGGACCGGATGACTTACCGTGTGAGGTCTCATGAAGGAGGCA
TCACCAAACCCTATACTTGCAGTGTTTGTGGGAAAGGCTTCTCAAGGCGCGACCCCTTAAGCTGTCATGTAAAACATGTC
CATTCAACAGAAAGACGCTTCAAATGCCAAACGTGCACTGCTGCCTTTGCCGCCAAAGACAGACTGCGGACACACATGGT
GTGCCACGAAGACAAGGTATCATGTAACATCTGTGGGAAGCTCCTGAGTGCAGCATACATCACCAGCCACTTAAAGACTC
ATGGGCAGAGCCAAAGTATCAACTGCAATCCATGTAAACAAGGCATCAGTAAAACATGCATGAGTGAAGAGACCAGTAAC
CAAAAGCAGCAGCAGCAAAAACAACAACAACAA

Alignment

ORF - retro_ptro_1961 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.86 %
• Parental protein coverage: 65.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASHHQQQAAQNSLLPLLSSAVEPPDQKPLLPIPITQKPQGAPETLKDAIGIKKEKPKTSFVCTYCSKAFR
          ASHHQQQAAQNSLLPLLSSAVE.PDQKPLLPIPITQKPQGAPETLKDAIGIKKEKPKTSFVCTYCSKAFR
Retrocopy ASHHQQQAAQNSLLPLLSSAVETPDQKPLLPIPITQKPQGAPETLKDAIGIKKEKPKTSFVCTYCSKAFR

Parental  DSYHLRRHESCHTGIKLVSRPKKTPTTVVPLISTIAGDSSRTSLVSTIAGILSTVTTSSSGTNPSSSAST
          DSYHLRRHESCHTGIK.VSRPKKTPTTV.PLISTIAGDSSRTSLVSTIAG.LSTVTTSSSGTNPSSSAST
Retrocopy DSYHLRRHESCHTGIKVVSRPKKTPTTVFPLISTIAGDSSRTSLVSTIAGVLSTVTTSSSGTNPSSSAST

Parental  TAMPVTQSVKKPSKPVKKNHACEMCGKAFRDVYHLNRHKLSHSDEKPFECPICNQRFKRKDRMTYHVRSH
          TA.PVTQSVKKPSKPVKKN.ACEMCGKAFRDVYHL..HKLSHSDEKPFECPICNQRFKRKDRMTY.VRSH
Retrocopy TALPVTQSVKKPSKPVKKNQACEMCGKAFRDVYHLSGHKLSHSDEKPFECPICNQRFKRKDRMTYRVRSH

Parental  EGGITKPYTCSVCGKGFSRPDHLSCHVKHVHSTERPFKCQTCTAAFATKDRLRTHMVRHEGKVSCNICGK
          EGGITKPYTCSVCGKGFSR.D.LSCHVKHVHSTER.FKCQTCTAAFA.KDRLRTHMV.HE.KVSCNICGK
Retrocopy EGGITKPYTCSVCGKGFSRRDPLSCHVKHVHSTERRFKCQTCTAAFAAKDRLRTHMVCHEDKVSCNICGK

Parental  LLSAAYITSHLKTHGQSQSINCNTCKQGISKTCMSEETSNQKQQQQQQQQQ
          LLSAAYITSHLKTHGQSQSINCN.CKQGISKTCMSEETSNQKQQQQ.QQQQ
Retrocopy LLSAAYITSHLKTHGQSQSINCNPCKQGISKTCMSEETSNQKQQQQKQQQQ

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	0.05 RPM	9.44 RPM
SRP007412_cerebellum	0.00 RPM	18.53 RPM
SRP007412_heart	0.00 RPM	20.55 RPM
SRP007412_kidney	0.00 RPM	30.02 RPM
SRP007412_liver	0.00 RPM	5.53 RPM
SRP007412_testis	0.00 RPM	29.61 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1961 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1961 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2902

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136451	1 retrocopy	retro_hsap_2902,
Nomascus leucogenys	ENSNLEG00000008084	1 retrocopy	retro_nleu_632,
Pan troglodytes	ENSPTRG00000009442	1 retrocopy	retro_ptro_1961 ,