RetrogeneDB ID: retro_pabe_750

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:19215054..19215354(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENY2
• Ensembl ID: ENSPPYG00000025888
• Aliases: None
• Description: enhancer of yellow 2 homolog (Drosophila) [Source:HGNC Symbol;Acc:24449]

Sequence

>retro_pabe_750
GTGGTTAGCAAGATGAACAAAGATGCGCAGATGAGAGAAGCCATTAACCAAAAGTTGATAGAAACTGGAGAAAGAGAATG
CTTCAAAGAGTTGCTGAGGGCTAAATTAATTGAATGTGGCTGGAAGGATCAGTTGAAGGCACACTGTAAACAGGTAATTA
AATAAAAAGGACTAGAACACATTACTGTTGATGACTTGGTGGCTGAAATCACTCCAAAAGGCAGAGCCCTGGTACCTGAC
AGTGTAAAGAAGGAGCTCCTACAAAGAATAAGAACGTTCCTTGCTCAGCATGCCAGCCTT

Alignment

ORF - retro_pabe_750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.0 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVSKMNKDAQMRAAINQKLIETGERERLKELLRAKLIECGWKDQLKAHCKEVIKEKGLEHVTVDDLVAEI
          VVSKMNKDAQMR.AINQKLIETGERE..KELLRAKLIECGWKDQLKAHCK.VIK.KGLEH.TVDDLVAEI
Retrocopy VVSKMNKDAQMREAINQKLIETGERECFKELLRAKLIECGWKDQLKAHCKQVIK*KGLEHITVDDLVAEI

Parental  TPKGRALVPDSVKKELLQRIRTFLAQHASL
          TPKGRALVPDSVKKELLQRIRTFLAQHASL
Retrocopy TPKGRALVPDSVKKELLQRIRTFLAQHASL

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	0.06 RPM	26.76 RPM
SRP007412_cerebellum	0.12 RPM	25.54 RPM
SRP007412_heart	0.09 RPM	21.55 RPM
SRP007412_kidney	0.20 RPM	37.95 RPM
SRP007412_liver	0.21 RPM	34.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_750 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_750 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1094

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003039	1 retrocopy	retro_acar_1,
Callithrix jacchus	ENSCJAG00000006389	4 retrocopies	retro_cjac_1206, retro_cjac_1355, retro_cjac_1436, retro_cjac_550,
Cavia porcellus	ENSCPOG00000010988	1 retrocopy	retro_cpor_927,
Dasypus novemcinctus	ENSDNOG00000007377	1 retrocopy	retro_dnov_25,
Echinops telfairi	ENSETEG00000010882	2 retrocopies	retro_etel_1826, retro_etel_450,
Microcebus murinus	ENSMICG00000012948	3 retrocopies	retro_mmur_1041, retro_mmur_773, retro_mmur_793,
Myotis lucifugus	ENSMLUG00000027585	1 retrocopy	retro_mluc_357,
Macaca mulatta	ENSMMUG00000006104	2 retrocopies	retro_mmul_1094, retro_mmul_1490,
Pongo abelii	ENSPPYG00000025888	1 retrocopy	retro_pabe_750 ,
Sarcophilus harrisii	ENSSHAG00000001787	4 retrocopies	retro_shar_454, retro_shar_675, retro_shar_815, retro_shar_816,
Tupaia belangeri	ENSTBEG00000000273	4 retrocopies	retro_tbel_2257, retro_tbel_324, retro_tbel_4307, retro_tbel_823,
Tursiops truncatus	ENSTTRG00000001742	3 retrocopies	retro_ttru_46, retro_ttru_845, retro_ttru_997,