RetrogeneDB ID: retro_pabe_2385

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:175974904..175975664(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BZW2
• Ensembl ID: ENSPPYG00000017763
• Aliases: None
• Description: basic leucine zipper and W2 domains 2 [Source:HGNC Symbol;Acc:18808]

Sequence

>retro_pabe_2385
CTAATGGCATCTATTCTTAATAGCCTTTATAATAAGAATTTGGTTAAAGAAGGGGTTTCAGCAGCTTTTGCTGTAAAGCT
CTTTAAATCATGAATAAATGAAAAAGATATCAATGCAGTAACTGCAAGGAAAGTCCGCATGGATAACAGCCTGATGGAAC
CTTTTCCTGCCAATAAGCAAAGCGTTAAACACTTCACAAAGTATTTTACTGAGGCAGGCCTGAAAGAGCTTTCAGAATAT
GTTTGGAATCAGCAAACCATCAGAGCTTGTAAGGAGCTCCAGAAAGAACTTCAAGAACAGATGTCCTGTGGGGATCCATT
TAAGGATATAATTTTATATGTCAAGGAGGAGATGAAAAAAAACAACATCCCAGAACCAGTTGTCATCCAAATAGTCTGGT
CAAATATAATGAGCGCCGTGGAATGGAACAAAAAAGAGGAGCTTGTAGCAGAGCAAGCCATCAGACACTTGAAGCAATAC
AGCCCTATACTTGCTGCCTTTACTACTCAAGGTCAGTCTGAGCTGACTGTTACTGAAGATTCAGGAGTATTGCTATGACA
ACATTCATTTCATGAAAGCCTTCCAGAAAATAGTGGTGCTTTTTTATAAAGCTATAGTCCTGAGCAAAGAGCCCATTTTG
AAGTGGTATAAAGGTACACATGTTGCAAAGGGGAAGAGTGTTTCCCTTGAGCAAATGAAAAAGTTTGGAGAGTGGCTCAA
AAATGCTGAAGAAGAATCTGAATCTGAAGCTGAAGAAAGT

Alignment

ORF - retro_pabe_2385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.93 %
• Parental protein coverage: 61.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPATILTSLFTDSLVKEGIAASFAVKLFKAWMAEKDANSVTSSLRKANLDKRLLELFPVNRQSVDHFAKY
          L.A.IL.SL....LVKEG..A.FAVKLFK....EKD.N.VT...RK...D..L.E.FP.N.QSV.HF.KY
Retrocopy LMASILNSLYNKNLVKEGVSAAFAVKLFKS*INEKDINAVTA--RKVRMDNSLMEPFPANKQSVKHFTKY

Parental  FTDAGLKELSDFLRVQQSLGTRKELQKELQERLSQECPIKEVVLYVKEEMKRNDLPETAVIGLLWTCIMN
          FT.AGLKELS.....QQ.....KELQKELQE..S...P.K...LYVKEEM.....PE..VI...W..IM.
Retrocopy FTEAGLKELSEYVWNQQTIRACKELQKELQEQMSCGDPFKDIILYVKEEMXXXNIPEPVVIQIVWSNIMS

Parental  AVEWNKKEELVAEQALKHLKQYAPLLAVFSSQGQSEL-ILLQKVQEYCYDNIHFMKAFQKIVVLFYKADV
          AVEWNKKEELVAEQA..HLKQY.P.LA.F..QGQSEL..LL.K.QEYCYDNIHFMKAFQKIVVLFYKA.V
Retrocopy AVEWNKKEELVAEQAIRHLKQYSPILAAFTTQGQSEL>LLL-KIQEYCYDNIHFMKAFQKIVVLFYKAIV

Parental  LSEEAILKWYKEAHVAKGKSVFLDQMKKFVEWLQNAEEESESEGEEN
          LS.E.ILKWYK..HVAKGKSV.L.QMKKF.EWL.NAEEESESE.EE.
Retrocopy LSKEPILKWYKGTHVAKGKSVSLEQMKKFGEWLKNAEEESESEAEES

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	0.33 RPM	14.93 RPM
SRP007412_cerebellum	0.85 RPM	7.17 RPM
SRP007412_heart	0.36 RPM	163.37 RPM
SRP007412_kidney	0.40 RPM	19.82 RPM
SRP007412_liver	0.49 RPM	11.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2385 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001663	4 retrocopies	retro_dnov_2177, retro_dnov_2422, retro_dnov_2649, retro_dnov_575,
Equus caballus	ENSECAG00000022038	1 retrocopy	retro_ecab_1121,
Macaca mulatta	ENSMMUG00000017045	1 retrocopy	retro_mmul_1457,
Ochotona princeps	ENSOPRG00000005256	2 retrocopies	retro_opri_665, retro_opri_9,
Pongo abelii	ENSPPYG00000017763	1 retrocopy	retro_pabe_2385 ,
Pteropus vampyrus	ENSPVAG00000014571	1 retrocopy	retro_pvam_481,
Ictidomys tridecemlineatus	ENSSTOG00000002506	1 retrocopy	retro_itri_1286,
Tarsius syrichta	ENSTSYG00000009806	1 retrocopy	retro_tsyr_1923,
Tursiops truncatus	ENSTTRG00000009867	1 retrocopy	retro_ttru_162,