RetrogeneDB ID: retro_ptro_3251

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:96271419..96271937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZRANB2
• Ensembl ID: ENSPTRG00000000856
• Aliases: None
• Description: None

Sequence

>retro_ptro_3251
GATAATGTTGAATATATAGAATGAGAAGAATCTGAAGGTAAATATGATGAGTTTGGATATAAAAAGAAAAAATGCAGAGG
GAAGCCTGTTGGTCCTGCATCTATATGAAAGGAGGTTGAAGTAAAGAATCAGAGGGAGAAGAAGAGGATGAGGATGAAGA
TCTTTCTAAATATAAATTAGATGAAGATGAGGATGAAGATGATGCTGATGTCTCAAAATATAATATTGACGTCAGTGAAG
AAGGCGATAGTAATAAAAAGAAATCTAATAGAAAAAGTCACTCAATATCTCAATCTTCACATTCACTATCTTCATCATGT
TCATTCTCCCTTTCAAATTCAAGGTCTAGGTCCAGGTTCCCTTCAAGAAGTTCTAGTTCACAGTCAAGATCTTGTTTCAG
TTCCAGAGAACATTTAAGATCCTCTGGGTTGAAATCAAGATCCAGTTCCAGGTCCCACAGGGGCTCACTAAACAACCCTG
AGCCCAGGGCCAACCCTTACTTTACCCAAGCACCACAG

Alignment

ORF - retro_ptro_3251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.57 %
• Parental protein coverage: 52.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ENVEYIEREESDGEYDEFGRKKKKYRGKAVGPASILKEVE-DKESEGEEEDEDEDLSKYKLDEDEDEDDA
          .NVEYIE.EES.G.YDEFG.KKKK.RGK.VGPASI.KEVE..KESEGEEEDEDEDLSKYK.........A
Retrocopy DNVEYIE*EESEGKYDEFGYKKKKCRGKPVGPASI*KEVE<SKESEGEEEDEDEDLSKYKXXXXXXXXXA

Parental  DLSKYNLDASEEEDSNKKKSNRRSRSKSRSSHSRSSSRSSSPSSSRSRSRSRSRSSSSSQSRSRSSSRER
          D.SKYN.D.SEE.DSNKKKSNR.S.S.S.SSHS.SSS.S.S.S.SRSRSR..SR.SSSSQSRS..SSRE.
Retrocopy DVSKYNIDVSEEGDSNKKKSNRKSHSISQSSHSLSSSCSFSLSNSRSRSRFPSR-SSSSQSRSCFSSREH

Parental  SRSRGSKSRSSSRSHRGS-SSPRKRSYSSSSSSPE
          .RS.G.KSRSSSRSHRGS...P..R........P.
Retrocopy LRSSGLKSRSSSRSHRGSLNNPEPRANPYFTQAPQ

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	55.37 RPM
SRP007412_cerebellum	0.00 RPM	84.93 RPM
SRP007412_heart	0.00 RPM	44.68 RPM
SRP007412_kidney	0.00 RPM	40.95 RPM
SRP007412_liver	0.00 RPM	23.57 RPM
SRP007412_testis	0.00 RPM	89.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3251 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3251 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2618

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006356	2 retrocopies	retro_cjac_2350, retro_cjac_4199,
Monodelphis domestica	ENSMODG00000000504	2 retrocopies	retro_mdom_1975, retro_mdom_443,
Oryctolagus cuniculus	ENSOCUG00000004640	2 retrocopies	retro_ocun_1170, retro_ocun_776,
Otolemur garnettii	ENSOGAG00000000485	4 retrocopies	retro_ogar_1274, retro_ogar_1841, retro_ogar_2843, retro_ogar_976,
Pan troglodytes	ENSPTRG00000000856	1 retrocopy	retro_ptro_3251 ,