RetrogeneDB ID: retro_pabe_2870

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:55300715..55301158(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRAS
• Ensembl ID: ENSPPYG00000004369
• Aliases: None
• Description: Kirsten rat sarcoma viral oncogene homolog [Source:HGNC Symbol;Acc:6407]

Sequence

>retro_pabe_2870
ATGACTGAATATAAACTTGCGGTAGTTGCAGCTGGTGGCGTAAGCAAGAGTGCCTTGACGATACAGCTAATTCAGAATCA
TTTTGTGGACGAATATGATCCAACAATAGAGGATTCCTACAGGAAGCAAGTAGTAATTGATGGAGAAACCTGTCTCTTGG
ATATTCTTGACACAGCAGGTAAAGCAGAGTACAATGCAATGAGGGACCAATACATGAGGACTGGGGGGGCTTTCTTTGTG
TATTTGCCATAAATAATATTAAATAATTTGAAGATATGCACAATTATAGAGAACAAATTAAAAGATTTAAGGACTCCGAG
ATGTGCCTATGGTCCTAGTAGGAAATAAATGTGATTTGCCTTCTAGAACAGTAGACACAAAAGGCTCAGGACTTAGCAAG
GAGTTAGGGAATTCCCTTTATTGAAACATCAGCAAAGACACGG

Alignment

ORF - retro_pabe_2870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 79.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
          MTEYKL.VV.AGGV.KSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG..EY.AMRDQ
Retrocopy MTEYKLAVVAAGGVSKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGKAEYNAMRDQ

Parental  YMRTG-EGFLCVFAINNTKSFEDIHHYREQIKRVKDSE-DVPMVLVGNKCDLPSRTVDTKQAQDLARSYG
          YMRTG..GFLCVFAINN.K.FED.H.YREQIKR.KDSE.DVPMVLVGNKCDLPSRTVDTK....L....G
Retrocopy YMRTG<GGFLCVFAINNIK*FEDMHNYREQIKRFKDSE<DVPMVLVGNKCDLPSRTVDTK-GSGLSKELG

Parental  -IPFIETSAKTR
          .IPFIETSAKTR
Retrocopy >IPFIETSAKTR

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	0.11 RPM	33.51 RPM
SRP007412_cerebellum	0.00 RPM	43.29 RPM
SRP007412_heart	0.00 RPM	10.54 RPM
SRP007412_kidney	0.00 RPM	18.60 RPM
SRP007412_liver	0.00 RPM	18.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2870 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2870 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3474

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000017458	1 retrocopy	retro_mdom_153,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pongo abelii	ENSPPYG00000004369	1 retrocopy	retro_pabe_2870 ,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,