RetrogeneDB ID: retro_pabe_3536

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:8331660..8332221(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019951
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNAQ
• Ensembl ID: ENSPPYG00000019311
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), q polypeptide [Source:HGNC Symbol;Acc:4390]

Sequence

>retro_pabe_3536
CTGCCTACGCAACAAGATGTGCTTAGAGTTCGAGTCCCCACCACAGGGATCATCGAATACCCCTTTGACTTACAAAGTGT
CATTTTCAGAATGTTCAAGGTAGGGGGCCAAAGGTCAGAGAGAAGAAAATGGACACACTGCTTTGAAAATGTCACCTCTA
TCATGTTTCTAGTAGTGCTTAGTGAATATGATCAAGTTCTCGTGGAATCAGACAATGAGAACCGAATGGAGGAAAGCAAG
GCTCTCTTTAGAACAATTAATCACATATCCCTGGTTCCAGAACTCCTCGGTTATTCTGTTCTTAAACAAGAAAGATCTTC
TAGAGGAGAAAATCATGTATTCCCATCTAGTCGACTACTTCCCAGAATATGATGGACCCCAGAGAGATGCCCAGGCAGCC
CGAGAATTCATTCTGAAGATGTTCGTGGACCTGAACCCAGACAGTGACAAAATTATCTACTCCCACTTCGCATGCGCCAC
AGACACCGAGATATCCGCTTTGTCTTTGCTGCCGTCAAGGACACCATCCTCCAGTTGAACCTGAAGGAGTACAATCTGGT
C

Alignment

ORF - retro_pabe_3536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.77 %
• Parental protein coverage: 52.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPTQQDVLRVRVPTTGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVES
          LPTQQDVLRVRVPTTGIIEYPFDLQSVIFRM..VGGQRSERRKW.HCFENVTSIMFLV.LSEYDQVLVES
Retrocopy LPTQQDVLRVRVPTTGIIEYPFDLQSVIFRMFKVGGQRSERRKWTHCFENVTSIMFLVVLSEYDQVLVES

Parental  DNENRMEESKALFRTI-ITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILK
          DNENRMEESKALFRTI.ITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILK
Retrocopy DNENRMEESKALFRTI>ITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILK

Parental  MFVDLNPDSDKIIYSHFTCATDTE-NIRFVFAAVKDTILQLNLKEYNLV
          MFVDLNPDSDKIIYSHF.CATDTE..IRFVFAAVKDTILQLNLKEYNLV
Retrocopy MFVDLNPDSDKIIYSHFACATDTE<DIRFVFAAVKDTILQLNLKEYNLV

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	0.66 RPM	45.01 RPM
SRP007412_cerebellum	0.49 RPM	12.89 RPM
SRP007412_heart	0.18 RPM	4.94 RPM
SRP007412_kidney	0.00 RPM	10.94 RPM
SRP007412_liver	0.00 RPM	2.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3536 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3536 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000002860	2 retrocopies	retro_nleu_2644, retro_nleu_2781,
Pongo abelii	ENSPPYG00000009366	1 retrocopy	retro_pabe_3045,
Pongo abelii	ENSPPYG00000019311	1 retrocopy	retro_pabe_3536 ,
Tupaia belangeri	ENSTBEG00000009447	2 retrocopies	retro_tbel_2487, retro_tbel_2974,