RetrogeneDB ID: retro_pabe_256

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:75903796..75904387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCCAG3
• Ensembl ID: ENSPPYG00000019772
• Aliases: None
• Description: serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]

Sequence

>retro_pabe_256
ATGTCTCCGGCCTCTCCGGCAGGGAGTCCTAGCGCAGACTTTGCGGCTCATGGAGAGTCTCTGGCAGACAGGCACCTGCG
GAAGCTGCAGATAAGTTACGAAGCACTGAAAGATGAAAATTCTAAGCTGAAAAGAAAACTGAATGAGGTTTAGAGCTTCT
CTGAAGCTCAAACAGAAATGCTGAGGACACTTGAGCGGAAATTAGAAGCAAAAATGATCAAGGAGGAAAGCGACTACCAC
GACTTGGAGTCGGTGGTTCAGCAGGTGGAGCAGAACCTGGAGCTGATGACCAAACGGGCTGTAAAGGCAGAAACCCACGT
CGTGAAACTGAAACAGGAAATCAATTTGCTCCAGGCGCAGGTCTCCAACTTCCAGCGAGAGAATGAAGCCCTGCGATGCG
GCCAGGGCGCCAGCCTGACAGTGGTGAAGCAGAACGCCGACGTGGCCTTGCAGAACCTCTGGGTGGTCGTGAACAGCGCA
CAGGCTTCCATTAAGCAACTGGTTTCCGGAGCTGAGACACAGAATCTTGGTGCCGAAATCCTTAAATCTATAGACAGAAT
TTCTGAAATTAAAGACGAGGAGGAAGACTCT

Alignment

ORF - retro_pabe_256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.39 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSPASPAGSPSADFAAHGESLGDRHLRTLQISYEALKDENSKLRRKLNEVQSFSEAQTEMVRTLERKLEA
          .SPASPAGSPSADFAAHGESL.DRHLR.LQISYEALKDENSKL.RKLNEV.SFSEAQTEM.RTLERKLEA
Retrocopy MSPASPAGSPSADFAAHGESLADRHLRKLQISYEALKDENSKLKRKLNEV*SFSEAQTEMLRTLERKLEA

Parental  KMIKEESDYHDLESVVQQVEQNLELMTKRAVKAENHVVKLKQEISLLQVQVSNFQRENEALRCSQGASLT
          KMIKEESDYHDLESVVQQVEQNLELMTKRAVKAE.HVVKLKQEI.LLQ.QVSNFQRENEALRC.QGASLT
Retrocopy KMIKEESDYHDLESVVQQVEQNLELMTKRAVKAETHVVKLKQEINLLQAQVSNFQRENEALRCGQGASLT

Parental  VVKQNADVALQNLRVVMNSAQASIKQLVSGAETLNVVAEILKSIDRISEIKDEEEDS
          VVKQNADVALQNL.VV.NSAQASIKQLVSGAET.N..AEILKSIDRISEIKDEEEDS
Retrocopy VVKQNADVALQNLWVVVNSAQASIKQLVSGAETQNLGAEILKSIDRISEIKDEEEDS

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	0.00 RPM	13.44 RPM
SRP007412_cerebellum	0.00 RPM	20.55 RPM
SRP007412_heart	0.00 RPM	4.79 RPM
SRP007412_kidney	0.00 RPM	25.62 RPM
SRP007412_liver	0.03 RPM	24.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_256 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_256 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000165689	1 retrocopy	retro_hsap_1944,
Gorilla gorilla	ENSGGOG00000010905	1 retrocopy	retro_ggor_1414,
Mus musculus	ENSMUSG00000026927	3 retrocopies	retro_mmus_1545, retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys	ENSNLEG00000008186	1 retrocopy	retro_nleu_891,
Otolemur garnettii	ENSOGAG00000015872	1 retrocopy	retro_ogar_3418,
Pongo abelii	ENSPPYG00000019772	2 retrocopies	retro_pabe_1612, retro_pabe_256 ,
Pan troglodytes	ENSPTRG00000021555	1 retrocopy	retro_ptro_1300,
Rattus norvegicus	ENSRNOG00000018876	2 retrocopies	retro_rnor_1215, retro_rnor_2770,