RetrogeneDB ID: retro_pabe_3321

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:43816769..43817117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB4A
• Ensembl ID: ENSPPYG00000000128
• Aliases: None
• Description: RAB4A, member RAS oncogene family [Source:HGNC Symbol;Acc:9781]

Sequence

>retro_pabe_3321
AATTGGTTAACAGATACCCAAATGCTAGTGAGTCAGAACATTGTGATCATCCTTTGTGGAAACAAGGAGGACCTGGATGC
AGATTGTGAAGTTATCTTCTTAGAAGACTCCAGATTTGCTCAAGAAAATGAGCTGATGTTTTTAGAAACAAGTGCACTAA
CAGGGGAGAATGTAGAAAAGGCTTTTGTACAGTGTGCAAGAAAAATACTTAACAAAATTCAATCAGGTGAGCTGGACCCA
GAAAGAATGGGCTCAGGTATTCAGTAGGGAGATGCTGCCTTGAGACAGCTGAGGTCACCATGGCACGCGGCCCAGGCACA
GGCCCCAAACTCTCAGGAATGTGGTTGT

Alignment

ORF - retro_pabe_3321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 51.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQENELMFLETSALTGENVEEAFVQCARKIL
          NWLTD..ML.SQNIVIILCGNK.DLDAD.EV.FLE.SRFAQENELMFLETSALTGENVE.AFVQCARKIL
Retrocopy NWLTDTQMLVSQNIVIILCGNKEDLDADCEVIFLEDSRFAQENELMFLETSALTGENVEKAFVQCARKIL

Parental  NKIESGELDPERMGSGIQYGDAALRQLRSP---RRAQAPNAQECGC
          NKI.SGELDPERMGSGIQ.GDAALRQLRSP.....AQAPN.QECGC
Retrocopy NKIQSGELDPERMGSGIQ*GDAALRQLRSPWHAAQAQAPNSQECGC

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	19.13 RPM
SRP007412_cerebellum	0.00 RPM	17.39 RPM
SRP007412_heart	0.00 RPM	6.41 RPM
SRP007412_kidney	0.00 RPM	9.28 RPM
SRP007412_liver	0.00 RPM	11.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3321 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3321 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013866	5 retrocopies	retro_chof_1017, retro_chof_1761, retro_chof_2377, retro_chof_64, retro_chof_703,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Macaca mulatta	ENSMMUG00000017720	1 retrocopy	retro_mmul_2336,
Nomascus leucogenys	ENSNLEG00000014339	1 retrocopy	retro_nleu_2062,
Pongo abelii	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321 ,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pongo abelii	ENSPPYG00000018056	1 retrocopy	retro_pabe_3574,