RetrogeneDB ID: retro_ptro_1716

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:177931430..177931661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBY1
• Ensembl ID: ENSPTRG00000014373
• Aliases: None
• Description: None

Sequence

>retro_ptro_1716
AGCCAGAAGTTTGAAAATGGCCGGTGGATAGCAGAGACAGGGATTAGTGGAGGTGTGGACCGGAGGGAGGCCCAGTGCCT
TCACAGGCAGAACTAGCAACTGGAGGAAGAGAACAGTCTCTTGCAGCTGAAAGTGGACATTCTGCTGGACATGTTTTCAG
AGACCACTGCTAAATCCCTTTTAATGGAGAAGGAAATGGATGCATGGAAGAGTGTCAGCCAGAGGAGAAAA

Alignment

ORF - retro_ptro_1716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLKFENGQWIAETGVSGGVDRREVQRLRRRNQQLEEENNLLRLKVDILLDMLSESTAESHLMEKELDELR
          S.KFENG.WIAETG.SGGVDRRE.Q.L.R.N.QLEEEN.LL.LKVDILLDM.SE.TA.S.LMEKE.D...
Retrocopy SQKFENGRWIAETGISGGVDRREAQCLHRQN*QLEEENSLLQLKVDILLDMFSETTAKSLLMEKEMDAWK

Parental  -ISRKRK
          ..S..RK
Retrocopy SVSQRRK

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	14.66 RPM
SRP007412_cerebellum	0.00 RPM	18.21 RPM
SRP007412_heart	0.00 RPM	12.47 RPM
SRP007412_kidney	0.00 RPM	24.90 RPM
SRP007412_liver	0.00 RPM	11.16 RPM
SRP007412_testis	0.11 RPM	17.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1716 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1716 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1716 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2344
Gorilla gorilla	retro_ggor_1781

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001384	2 retrocopies	retro_cfam_1396, retro_cfam_852,
Dasypus novemcinctus	ENSDNOG00000010982	1 retrocopy	retro_dnov_875,
Homo sapiens	ENSG00000100211	1 retrocopy	retro_hsap_2344,
Gorilla gorilla	ENSGGOG00000013226	1 retrocopy	retro_ggor_1781,
Myotis lucifugus	ENSMLUG00000003757	2 retrocopies	retro_mluc_1128, retro_mluc_2608,
Mustela putorius furo	ENSMPUG00000013150	1 retrocopy	retro_mputfur_1186,
Nomascus leucogenys	ENSNLEG00000015153	1 retrocopy	retro_nleu_349,
Otolemur garnettii	ENSOGAG00000028533	1 retrocopy	retro_ogar_1072,
Pan troglodytes	ENSPTRG00000014373	1 retrocopy	retro_ptro_1716 ,
Vicugna pacos	ENSVPAG00000001484	1 retrocopy	retro_vpac_57,