RetrogeneDB ID: retro_ptro_1990

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:55986467..55987139(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90B
• Ensembl ID: ENSPTRG00000004129
• Aliases: None
• Description: None

Sequence

>retro_ptro_1990
CTGCAGAGAGACTTCTTCAGCACCACAACCAAGGAGGGATATGATAGGCTGCCAGTGGATATAACTCCTTTAGAAGAAAG
GAAATTAACTTTTGATACCCATGCGTTGGTTCAGGACTTGGAAACTCTTGGATTTGACAAAACACAAGCAGAAACAACAG
TATCAGCATTAACTACTTTATCAAATGTCAGCCCGGATACTACCTATAAAGAGACGGTCACTCAAGCTCAACAGAAAATA
ACAGTACAACAGCTAATGGCTCATTTGGACTCTATCAGGAAAAACATGGTCAGCCTAGAGAAAAGTGAATTCACAAATCT
CAGAGCAGAGAATGAGAAAATGAAAATTGAATTAGACCAAGTTAAGCAACAACTAATACATGAAACCAGTTGAATCAGAG
CAAATAATAAACTGGATATCAACCTAGAAAGGAGCAGAGTAACAGATATGTTTACAGATCAAGAAAAGCAACTTATGGAA
GCAACTACAGAATTTACAAAAAAGGATACCCAAACCAAAAGTATTATTTCAGAGACCAGTAATAAAATTGACGCAGAAAT
TGCTTCCTTAAAAACACTGATGGAGTCTAACAAACTTGAGACAATTCGTTATCTTGCAGCCTTGGTGTTTATTTGCCTGG
CAATAGCATTGGGATTTTATAGATTCTGAAAG

Alignment

ORF - retro_ptro_1990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.18 %
• Parental protein coverage: 88.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRREFFTTTTKEGYDRRPVDITPLEQRKLTFDTHALVQDLETHGFDKTQAETIVSALTALSNVSLDTIYK
          L.R.FF.TTTKEGYDR.PVDITPLE.RKLTFDTHALVQDLET.GFDKTQAET.VSALT.LSNVS.DT.YK
Retrocopy LQRDFFSTTTKEGYDRLPVDITPLEERKLTFDTHALVQDLETLGFDKTQAETTVSALTTLSNVSPDTTYK

Parental  EMVTQAQQEITVQQLMAHLDAIRKDMVILEKSEFANLRAENEKMKIELDQVKQQLMHETSRIRADNKLDI
          E.VTQAQQ.ITVQQLMAHLD.IRK.MV.LEKSEF.NLRAENEKMKIELDQVKQQL.HETS.IRA.NKLDI
Retrocopy ETVTQAQQKITVQQLMAHLDSIRKNMVSLEKSEFTNLRAENEKMKIELDQVKQQLIHETS*IRANNKLDI

Parental  NLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKLETIRYLAASVF
          NLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKLETIRYLAA.VF
Retrocopy NLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKLETIRYLAALVF

Parental  TCLAIALGFYRFWK
          .CLAIALGFYRF.K
Retrocopy ICLAIALGFYRF*K

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	0.05 RPM	10.92 RPM
SRP007412_cerebellum	0.00 RPM	8.28 RPM
SRP007412_heart	0.03 RPM	8.16 RPM
SRP007412_kidney	0.03 RPM	11.43 RPM
SRP007412_liver	0.00 RPM	7.40 RPM
SRP007412_testis	0.00 RPM	63.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1990 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1990 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3050
Pongo abelii	retro_pabe_2525

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880, retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990 ,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366,