RetrogeneDB ID: retro_ptro_2204

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:156352516..156353656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIG
• Ensembl ID: ENSPTRG00000012617
• Aliases: None
• Description: None

Sequence

>retro_ptro_2204
AGTGCATCTAGTAAGAGTGAAGCTGAAAATCATAGAGCACAACCCCAGTCTACTGTCCATCCAGAAGAGATCCCTCCTAT
ACCTGAAAATATATTTCCTAATGAGAAAAAGTCCTCCTAAAGCTGATGCAATGGAAAGGAAAAGCCAGAGAGAGAGAAAG
AGAAACAGAATGTAATCCATCTAACTCCCAGCCTGCTTCATACCAGAGACGACTTTTAGTTACTAGATCTGGCAGGAGAA
TTAAAGGAAGAGGATCAAGGTGTTATCAAACTCCTTCCAGATCCAGATCAAGGGATTGTTTCAGACTTAGTGAGACTCCT
GCACGTTGGAGGCAAGAGATGCAGAGAGTTCAAAGGATGAGGGCATCAAGTGGTGAAAGATGGATCAAAGGGGATAAGAG
TGAGTTGAATGAAATAAAAGAAAATCAGAGAAGTCTAGTTAGAGTAAAAGAGAGAAAAATAACTAACCACAGGAATGTAT
TTGAGAGTCCAAACAGAAAAAATGAAAAGGAAAAGAAAGCTAAAGACTGTAAATCTAACAGCAAAGAGAGACATCAGAAG
AAATTCAGAAAAAGATGATAAATATAATACGAACAAAGTGAAGAAAAGAGCCAAATCTAAAATTAAGAGTAAGAGCAAAG
AGAAATCAAAGAGTAAAGAAGGAGATTCAAGACATAATAGACATGAAGAAAAGAGGATGAGGTCAAGGAGCAAAGGAAGG
GATTATGTGAATGTTAAAGAAAAAGAAAAGGAGCTTGATTCAAAAGGAAACAATCAGGAAAGGGGTAGAAGTAAAGAGAA
GTCTAAACAGTTAGAATCAAAGAGTAATGAGCATGATCATAGTAAAACTAAGGAAAAGGATAGATGTGCACAATCCAGGA
GTAGAGAATGTGATATAACTGAAGGTAAACACAGTTATAATAGCAGAACAGGAGAGCAAAGCAGAAGTAGGGACAGAAGC
AGAAGAGTGTGATCAAGAAGCCATGACAGAGATTGCAGCAGAAGCAAGGAGTACCATAGATACAGAGGAAAGGAATACAG
GAGAAGAGGACAGTCACAAAGCCGAGGGAGAAGAACACCACCAGGAAGATCAAGAAGTAGAGATAGGGGTAGAAGGAGGA
GAGACTCACGGAGCTCAGAG

Alignment

ORF - retro_ptro_2204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.55 %
• Parental protein coverage: 50.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SASSESEAENLEAQPQSTVRPEEIPPIPEN-RFLMRKSPPKADEKERKN-RERERERECNPPNSQPASYQ
          SASS.SEAEN..AQPQSTV.PEEIPPIPEN..FLMRKSPPKAD..ERK..RERERE.ECNP.NSQPASYQ
Retrocopy SASSKSEAENHRAQPQSTVHPEEIPPIPEN>YFLMRKSPPKADAMERKS>RERERETECNPSNSQPASYQ

Parental  RRLLVTRSGRKIKGRGPRRYRTPSRSRSRDRFRRSETPPHWRQEMQRAQRMRVSSGERWIKGDKSELNEI
          RRLLVTRSGR.IKGRG.R.Y.TPSRSRSRD.FR.SETP..WRQEMQR.QRMR.SSGERWIKGDKSELNEI
Retrocopy RRLLVTRSGRRIKGRGSRCYQTPSRSRSRDCFRLSETPARWRQEMQRVQRMRASSGERWIKGDKSELNEI

Parental  KENQRSPVRVKERKITDHRNVSESPNRKNEKEK-KVKDHKSNSKERDIRRNSEKDDKYK-NKVKKRAKSK
          KENQRS.VRVKERKIT.HRNV.ESPNRKNEKEK.K.K......K.RDIRRNSEKDDKY..NKVKKRAKSK
Retrocopy KENQRSLVRVKERKITNHRNVFESPNRKNEKEK>KLKTVNLTAK-RDIRRNSEKDDKYNTNKVKKRAKSK

Parental  SRSKSKEKSKSKERDSKHNRNEEKRMRSRSKGRDHENVKEKEKQSDSKGKDQERSRSKEKSKQLESKSNE
          ..SKSKEKSKSKE.DS.HNR.EEKRMRSRSKGRD..NVKEKEK..DSKG..QER.RSKEKSKQLESKSNE
Retrocopy IKSKSKEKSKSKEGDSRHNRHEEKRMRSRSKGRDYVNVKEKEKELDSKGNNQERGRSKEKSKQLESKSNE

Parental  HDHSKSKEKDRRAQSRSRECDITKGKHSYNSRTRERSRSRDRSRRVRSRTHDRDRSRSKEYHRYREQEYR
          HDHSK.KEKDR.AQSRSRECDIT.GKHSYNSRT.E.SRSRDRSRRV.SR.HDRD.SRSKEYHRYR..EYR
Retrocopy HDHSKTKEKDRCAQSRSRECDITEGKHSYNSRTGEQSRSRDRSRRV*SRSHDRDCSRSKEYHRYRGKEYR

Parental  RRGRSRSRERRTPPGRSRSKDRRRRRRDSRSSE
          RRG.S.SR.RRTPPGRSRS.DR.RRRRDSRSSE
Retrocopy RRGQSQSRGRRTPPGRSRSRDRGRRRRDSRSSE

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	27.03 RPM
SRP007412_cerebellum	0.07 RPM	52.30 RPM
SRP007412_heart	0.23 RPM	46.75 RPM
SRP007412_kidney	0.03 RPM	31.43 RPM
SRP007412_liver	0.00 RPM	29.26 RPM
SRP007412_testis	0.11 RPM	65.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2204 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003185	1 retrocopy	retro_ggor_2220,
Pan troglodytes	ENSPTRG00000012617	1 retrocopy	retro_ptro_2204 ,