RetrogeneDB ID: retro_ptro_1761

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:21772919..21773387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VENTX
• Ensembl ID: ENSPTRG00000003087
• Aliases: None
• Description: VENT homeobox [Source:HGNC Symbol;Acc:13639]

Sequence

>retro_ptro_1761
GGGAGCCTCCCTGGCCCGGGCCAGACATTCCGCACCCGGGAGCCCCCTCAGGCTGTCAGTACCAAGGAGGCTAGCTCGTC
AAATCTGCATGCGCCGGAGAGGACTGTGGCTGGGTTGAGTAAGGAGCCAAACCCCTAGCTGGCTCCCGGTGTCCGCACAG
CCTTCACCACGGAGCAGGTCCGTGCCTTGGAGGGCGTCTTCCGGCACCACCAGTACCTGGGCCCTCTGGAGCGGAATTGG
CTGGCCAGGGAGATGCAGCTCTCAGAGGTCCAGATAAAAACCTGGTTTCAAAATCGCCGGATGAAACACAAACGGCAAAT
GCAGGACTCCCAGCTAAACGGCCCCTTATCAGGGTCTCTCCACGGGCCCCCTGCTTTCCACTCACCATCTTCTCGCCTTG
CCAATGGCCTGCAGCTGCTGTGCCCTTGGGCACCCCTGCCTGGGCCCCCTGGCTGCCCCTTGGCTCCT

Alignment

ORF - retro_ptro_1761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.62 %
• Parental protein coverage: 60.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSLPGPGQTSGAREPPQAVSIKEAARSSNLPAPERTVAGLSKEPNTLRVPRVRTAFTMEQVRTLEGVFQH
          GSLPGPGQT...REPPQAVS.KEA..SSNL.APERTVAGLSKEPN....P.VRTAFT.EQVR.LEGVF.H
Retrocopy GSLPGPGQTFRTREPPQAVSTKEAS-SSNLHAPERTVAGLSKEPNP*LAPGVRTAFTTEQVRALEGVFRH

Parental  HQYLSPLERKRLAREMQLSEVQIKTWFQNRRMKHKRQMQDPQLHSPFSGSLPAPPAFYSPSSGLANGLQL
          HQYL.PLER..LAREMQLSEVQIKTWFQNRRMKHKRQMQD.QL..P.SGSL..PPAF.SPSS.LANGLQL
Retrocopy HQYLGPLERNWLAREMQLSEVQIKTWFQNRRMKHKRQMQDSQLNGPLSGSLHGPPAFHSPSSRLANGLQL

Parental  LCPWAPLSGPQALMLPP
          LCPWAPL.GP....L.P
Retrocopy LCPWAPLPGPPGCPLAP

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	0.04 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1761 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1761 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2612
Gorilla gorilla	retro_ggor_1830
Macaca mulatta	retro_mmul_1477

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151650	4 retrocopies	retro_hsap_1027, retro_hsap_2612, retro_hsap_3973, retro_hsap_4038,
Gorilla gorilla	ENSGGOG00000003340	3 retrocopies	retro_ggor_1830, retro_ggor_2668, retro_ggor_2708,
Macaca mulatta	ENSMMUG00000000543	2 retrocopies	retro_mmul_1477, retro_mmul_2294,
Nomascus leucogenys	ENSNLEG00000002047	5 retrocopies	retro_nleu_2033, retro_nleu_2054, retro_nleu_635, retro_nleu_664, retro_nleu_905,
Pan troglodytes	ENSPTRG00000003087	4 retrocopies	retro_ptro_1761 , retro_ptro_2698, retro_ptro_2736, retro_ptro_702,