RetrogeneDB ID: retro_pabe_458

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:151944329..151944908(-)
• Located in intron of: ENSPPYG00000001225

Retrocopy information

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

Parental gene information

• Parental gene symbol: AARSD1
• Ensembl ID: ENSPPYG00000029909
• Aliases: None
• Description: alanyl-tRNA synthetase domain containing 1 [Source:HGNC Symbol;Acc:28417]

Sequence

>retro_pabe_458
GACCTTCAGGTCATCAAGATTCTGGGCACTGAGAAAGGGAAAAAGAACAAAACCAACCTGATATTTCTGACTGGGAACCA
GGTGGTGAAGTGGATGGAGAGAACTCATGAAACTGAAAAAGCACTGACTACTCTGCTTAAGTGTGGAGCAGAGGATCACG
TGGAAGCAGTGAAAAAGCTCCAGAACTCCACCAAGCTCCTGCAGAAGAATAACCTGAATCTGCTCAGAGACCTGGCTGTG
CATATTGCCCATAGCAGGAACAACCCAGACTGGTGAGGTGTGGTCATATTACACAGGAAGGAGGGTGATTCAGAGTTCAT
GAATATCACTGCCAATGAGATTGGGTCAGAGGAGACCCTCCTGTTCTTAACCGTGGGCAATGAGAAAGGTGCTGGGCTCT
TCTTACTGGCAGGGCGACCTGCAGCTGTGGAGACCCTGGGGCCCAGGGTGGCTGAGGTCCTGGAAGGCAAAGGAGCAAGG
AAGAAAGGCTGTTTTCAGGGTAAGGCCACCAAGCTGAGCCAGCGGGCGGAGGCACAGGTGCTTCTCCAGGACTACATCAG
CACACAGAGTGCTAAGGAG

Alignment

ORF - retro_pabe_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.63 %
• Parental protein coverage: 72.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLQVIKILGTEKGKKNKTNLIFLAGNRVLKWMERSHGTEKALTALLKCGAEDHVEAVKKLQNSTKILQKN
          DLQVIKILGTEKGKKNKTNLIFL.GN.V.KWMER.H.TEKALT.LLKCGAEDHVEAVKKLQNSTK.LQKN
Retrocopy DLQVIKILGTEKGKKNKTNLIFLTGNQVVKWMERTHETEKALTTLLKCGAEDHVEAVKKLQNSTKLLQKN

Parental  NLNLLRDLAVHIARRLRNSPDWGGVVVLHRKEGDSEFMNIIANEIGSEETLLFLTVGDEKGAGLFLLAGP
          NLNLLRDLAVHIA...RN.PDW.GVV.LHRKEGDSEFMNI.ANEIGSEETLLFLTVG.EKGAGLFLLAG.
Retrocopy NLNLLRDLAVHIAHS-RNNPDW*GVVILHRKEGDSEFMNITANEIGSEETLLFLTVGNEKGAGLFLLAGR

Parental  PASVETLGPRVAEVLEGKGAGKKGRFQGKATKMSRRMEAQALLQDYISIQSAKE
          PA.VETLGPRVAEVLEGKGA.KKG.FQGKATK.S.R.EAQ.LLQDYIS.QSAKE
Retrocopy PAAVETLGPRVAEVLEGKGARKKGCFQGKATKLSQRAEAQVLLQDYISTQSAKE

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	0.55 RPM	27.98 RPM
SRP007412_cerebellum	0.73 RPM	18.48 RPM
SRP007412_heart	0.24 RPM	11.05 RPM
SRP007412_kidney	0.53 RPM	17.67 RPM
SRP007412_liver	0.46 RPM	14.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_458 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000266967	1 retrocopy	retro_hsap_4707,
Pongo abelii	ENSPPYG00000004669	4 retrocopies	retro_pabe_2010, retro_pabe_2579, retro_pabe_5, retro_pabe_553,
Pongo abelii	ENSPPYG00000029909	3 retrocopies	retro_pabe_3654, retro_pabe_3655, retro_pabe_458 ,
Ictidomys tridecemlineatus	ENSSTOG00000000481	1 retrocopy	retro_itri_940,