RetrogeneDB ID: retro_ptro_1332

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:40020658..40021241(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF396
• Ensembl ID: ENSPTRG00000009970
• Aliases: None
• Description: zinc finger protein 396 [Source:HGNC Symbol;Acc:18824]

Sequence

>retro_ptro_1332
CCCCACCACGAAGAGTGTCCACAAGGAGAGCTCCAGCTTCTCTGACTGAGGCCGGAGGTGCACACAAAGGGGCAGATCCT
GGAGCTGCTGGTGCTGGAGCAGTTCCTGGCCATCCTCCCAGAAAAGCTGCAGCCCTGGGTGCTGAGGCATCATCCAGAAA
ATGGAGAGGAAGCTGTGACTATGCTGGAGGATGTGCAGAGAGAGCTTGATGGACCAAAGCAGGTCTTCTTTTTTGGACGA
AGAAAGGGACACGGTTGCAGAGAAGCTAGCACCTTCAGAAATCACTGAGCAATTGCCAACTAGCCAGCACACGCCCGTGA
AGAAGCAGCTCCAGCGAAAATCATGGGAGCTGCAGTCCTTAAGACCACATGATGAAGACATCAAAACTATAAATGTGAAA
TCCGCTTCAAGGCAAAAGACTTCTTCAGGCATAGAACTGCATTGCGATGTTTTGAACATCCTCGGTATAAATCCCTCCCA
GAGTTCCACATATAGAGGAATGTATGAACAAGATGATTCAAAATATGAACACAGGATTGCAGAGTCCCAAAAGAATATGT
ACTTCAAGACTAGGCTGAAGTGT

Alignment

ORF - retro_ptro_1332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.82 %
• Parental protein coverage: 56.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PHEALSRLRELCHLWLRPEVHTKEQILELLVLEQFLAILPKELQAWVQKHHPENGEETVTMLEDVERELD
          PH.......EL..L.LRPEVHTK.QILELLVLEQFLAILP..LQ.WV..HHPENGEE.VTMLEDV.RELD
Retrocopy PHHEECPQGELQLL*LRPEVHTKGQILELLVLEQFLAILPEKLQPWVLRHHPENGEEAVTMLEDVQRELD

Parental  GPKQIFF-GRRK-DMIAEKLAPSEITEELPSSQLMPVKKQLQGASWELQSLRPHDEDIKTTNVKSASRQK
          GPKQ.FF.GRRK.D..AEKLAPSEITE.LP.SQ..PVKKQLQ..SWELQSLRPHDEDIKT.NVKSASRQK
Retrocopy GPKQVFFFGRRK>DTVAEKLAPSEITEQLPTSQHTPVKKQLQRKSWELQSLRPHDEDIKTINVKSASRQK

Parental  TSLGIELHCSVSNILHMNASQSSTYRGTYEQ-DGRFEKR----QGNPSWKKQQKC
          TS.GIELHC.V.NIL..N.SQSSTYRG.YEQ.D...E.R....Q.N...K...KC
Retrocopy TSSGIELHCDVLNILGINPSQSSTYRGMYEQDDSKYEHRIAESQKNMYFKTRLKC

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	1.22 RPM
SRP007412_cerebellum	0.00 RPM	0.75 RPM
SRP007412_heart	0.00 RPM	0.52 RPM
SRP007412_kidney	0.00 RPM	3.69 RPM
SRP007412_liver	0.00 RPM	0.72 RPM
SRP007412_testis	0.11 RPM	7.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1332 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1332 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1996
Gorilla gorilla	retro_ggor_1443

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186496	1 retrocopy	retro_hsap_1996,
Gorilla gorilla	ENSGGOG00000023692	1 retrocopy	retro_ggor_1443,
Pongo abelii	ENSPPYG00000009107	1 retrocopy	retro_pabe_1637,
Pan troglodytes	ENSPTRG00000009970	1 retrocopy	retro_ptro_1332 ,