RetrogeneDB ID: retro_pabe_3719

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:8517804..8518527(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRAXIN
• Ensembl ID: ENSPPYG00000001884
• Aliases: None
• Description: dorsal inhibitory axon guidance protein [Source:HGNC Symbol;Acc:25054]

Sequence

>retro_pabe_3719
CTAGTCCTAGTCCTCCTGCTGCCCCTGGAGCTGAGCCTGGCAAACGCCCTTGCACCTGGGACCCCTGCTCAGAATCTACC
CGAGAATCACATCGACCTCCCAGGCCCAGCGCTGTGGTCGCCTCAGGCCAGCCACCGCCGCCAGCGCGACCCGGGCAAGA
AGGAGTGGGGCTCAGGCCTGCCCAGGTAGGCCCAGGATAGGGCTGTGCTCACCGCCACCAGGCAGGCTTCCAGGCTGCCA
GGGCCTGAGGGGCCGCTGCCTGAGCAGAGTCCTGCAGGCCTGCTGCGGGTCAAGGACCTGCTCCTGGGGCTCGAGTTGCC
CTACCCCAAGAAGGAGAATCGGTGTCCAGGGTGGGAGAGGGCCAGGAAACGCAGCAGGGAGTACAAGAGACGCAGGGACA
GGCTGAGGCTGCACCGAGGCCGAGCCTTGGTCGGAGGTCCCAGTTACCTGATGAAGGCAGAGCTTTCCGAAGCCAAGGCG
CTGGATGCGACCATGAAGGATTCTTCCGCCAGTCTGGCCCCCACCATGCTCTTCCTCACGACCTTTGAGGCAGCACCTGC
CACAGAAGAGTCCTTAATCTTGCTCATCGCCCCCCTGCGGCCCCAGGCACAGCACAGGCCTGACGGGGAGGCGATACCCA
CACTGGACGTGGCCTTGTTCGACTGGACCGATTATGAAGACTTAAAACCTGATGGCGGGCCCTCTGCAAAGAAGAAAGAA
AAA

Alignment

ORF - retro_pabe_3719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 69.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFFVLLLPLELSLADALALGTPAWNLPENHIDLPGPALWTPQASHYRRRGPGKKEWGPGLPSQAQDGAVA
          L..VLLLPLELSLA.ALA.GTPA.NLPENHIDLPGPALW.PQASH.R.R.PGKKEWG.GLP..AQD.AV.
Retrocopy LVLVLLLPLELSLANALAPGTPAQNLPENHIDLPGPALWSPQASHRRQRDPGKKEWGSGLPR*AQDRAVL

Parental  TTTRQASRLPEAEGLLPEQSPAGLLQDKDLLLGLALPYPEKENRPPGWERTRKRSREHKRRRDRLRLHRG
          T.TRQASRLP..EG.LPEQSPAGLL..KDLLLGL.LPYP.KENR.PGWER.RKRSRE.KRRRDRLRLHRG
Retrocopy TATRQASRLPGPEGPLPEQSPAGLLRVKDLLLGLELPYPKKENRCPGWERARKRSREYKRRRDRLRLHRG

Parental  RALVRGPSSLMKKAEFSEAQVLDAAMEESSTSLAPTMFFLTTFEAAPATEESLILPVTSLRPQQAQPRSD
          RALV.GPS.LM.KAE.SEA..LDA.M..SS.SLAPTM.FLTTFEAAPATEESLIL....LRP.QAQ.R.D
Retrocopy RALVGGPSYLM-KAELSEAKALDATMKDSSASLAPTMLFLTTFEAAPATEESLILLIAPLRP-QAQHRPD

Parental  GEVMPTLDMALFDWTDYEDLKPDGWPSAKKKEK
          GE..PTLD.ALFDWTDYEDLKPDG.PSAKKKEK
Retrocopy GEAIPTLDVALFDWTDYEDLKPDGGPSAKKKEK

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	0.28 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3719 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3719 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3719 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4779
Macaca mulatta	retro_mmul_2550

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000162490	1 retrocopy	retro_hsap_4779,
Macaca mulatta	ENSMMUG00000001652	1 retrocopy	retro_mmul_2550,
Pongo abelii	ENSPPYG00000001884	1 retrocopy	retro_pabe_3719 ,
Pan troglodytes	ENSPTRG00000000150	1 retrocopy	retro_ptro_3065,