RetrogeneDB ID: retro_pabe_2525

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:77365525..77366197(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90B
• Ensembl ID: ENSPPYG00000003736
• Aliases: None
• Description: coiled-coil domain containing 90B [Source:HGNC Symbol;Acc:28108]

Sequence

>retro_pabe_2525
CTGCGGAGAGACTTCTTCAGCACCACAACCAAGGAGGGATATGATAGGCCGCCAGTGGATATAACTCCTTTAGAAGAAAG
GAAGTTAACTTTTGATATCCATGCATTGGTTCAGGACTTGGAAACTCATGGATTTGACAAAACACAAGCAGAAACAATAG
TATCAGCATTAACTACTTTATCAAATGTCAGCCCGAATACTACCTGTAAAGAGATGGTCGCTCAAGCTCAACAGAAAATA
ACAGTACAACAGCGAATGGCTTATTTGGACTCTATCAGAAAAGACATGGTCGTCCTAGAGAAAAGTGAATTCACAAATCT
GAGAGCAGAGAATGAGAAAATGAAAATTGAATTAAACCAAGTTAAGCAACAACTAATACATGAAACCAGTTGAATCAGAG
CAGATAATAAACTGGATATCAACCTAGAAAGGAGCAGAGTAACAGATATGTTTACAGATCAAGAAAAGCAACTTATGGAA
GCAACTACAGAATTTACAAAAAAGGATACCCAAACCAAAAGTATTATTTCAGAGACCAGTAATAAAATTGACGCAGAAAT
TGCTTCCTTAAAAACACTGATGGAGTCTAACAAACTTAACACAATTCATCACCTTTCAGCCTTGGTGTTTATTTGCCTGG
CAATAGCATTGGGATTTTTTAGATTCTGGAAG

Alignment

ORF - retro_pabe_2525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 88.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRREFFTTTTKEGYDRRPVDITPLEQRKLTFDTHALVQDLETHGFDKSQAETIVSALTTLSNVSLDTIYK
          LRR.FF.TTTKEGYDR.PVDITPLE.RKLTFD.HALVQDLETHGFDK.QAETIVSALTTLSNVS..T..K
Retrocopy LRRDFFSTTTKEGYDRPPVDITPLEERKLTFDIHALVQDLETHGFDKTQAETIVSALTTLSNVSPNTTCK

Parental  EMVTQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAENEKMKIELDQIKQQLMHETSRIRADNKLDI
          EMV.QAQQ.ITVQQ.MA.LDSIRKDMV.LEKSEF.NLRAENEKMKIEL.Q.KQQL.HETS.IRADNKLDI
Retrocopy EMVAQAQQKITVQQRMAYLDSIRKDMVVLEKSEFTNLRAENEKMKIELNQVKQQLIHETS*IRADNKLDI

Parental  NLERSRVTDMFTDQEKQLMETTTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKLETIRYLAASVF
          NLERSRVTDMFTDQEKQLME.TTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKL.TI..L.A.VF
Retrocopy NLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKLNTIHHLSALVF

Parental  TCLAIALGFYRFWK
          .CLAIALGF.RFWK
Retrocopy ICLAIALGFFRFWK

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	12.00 RPM
SRP007412_cerebellum	0.00 RPM	16.78 RPM
SRP007412_heart	0.00 RPM	4.43 RPM
SRP007412_kidney	0.00 RPM	7.46 RPM
SRP007412_liver	0.00 RPM	7.22 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2525 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2525 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3050
Pan troglodytes	retro_ptro_1990

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 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,
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,