RetrogeneDB ID: retro_pabe_3654

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:71513238..71513644(+)
• Located in intron of: None

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_3654
GTGAATGCAGAGAAAATAAATGCCACTGAAAAGAGTGTCAATAAAAATATCAGAGATCAGCTGCTCAACAAAGTATGAGA
ACTGAGCCTGAATGATTCTGAGGCGGAGCAGGTGAGAGGCTGGGGCCTGCCAGATGATCATGCTGGGCCCATTGGAATTG
TTACCATCAAGGGTGTTGATTCCAACATGTGCTGTGGGATCCCCATGAGCAATCTCCGTGACTTTCCAGTCATTAAGATT
CTAGGCACTGAGAAGAGGAAAAGGAATAAAATCAAACTGATATTTCAGTCTGGGAACCAGATGCTGAAATGGATGAAGAG
AAGTCATGAAACTGAAAAAGCACTGAATCACTCTGCTTAAGTGTGGAGCAGAGGATCACATGGAAGCAGTGAAAAAGCTC
CAGAAT

Alignment

ORF - retro_pabe_3654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.85 %
• Parental protein coverage: 50.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTAEQVAAIEQSVNEKIRDRLPVNVRELSLDDPEVEQVRGRGLPDDHAGPIRVVSIKGVDSNMCCGTHVS
          ..AE...A.E.SVN..IRD.L...V.ELSL.D.E.EQVRG.GLPDDHAGPI..V.IKGVDSNMCCG...S
Retrocopy VNAEKINATEKSVNKNIRDQLLNKV*ELSLNDSEAEQVRGWGLPDDHAGPIGIVTIKGVDSNMCCGIPMS

Parental  NLSDLQVIKILGTEKGKKNKTNLIFLAGNRVLKWMERSHGTEKALT-ALLKCGAEDHVEAVKKLQN
          NL.D..VIKILGTEK.K.NK..LIF..GN..LKWM.RSH.TEKAL...LLKCGAEDH.EAVKKLQN
Retrocopy NLRDFPVIKILGTEKRKRNKIKLIFQSGNQMLKWMKRSHETEKALN>TLLKCGAEDHMEAVKKLQN

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	0.50 RPM	27.98 RPM
SRP007412_cerebellum	0.12 RPM	18.48 RPM
SRP007412_heart	0.00 RPM	11.05 RPM
SRP007412_kidney	0.23 RPM	17.67 RPM
SRP007412_liver	0.09 RPM	14.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3654 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3654 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,