RetrogeneDB ID: retro_pabe_2922

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:157919389..157919806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf203
• Ensembl ID: ENSPPYG00000016885
• Aliases: None
• Description: chromosome 6 open reading frame 203 [Source:HGNC Symbol;Acc:17971]

Sequence

>retro_pabe_2922
GATGAGGAGGACTCTGATGCAGAAAGTGATCAGAACGAGATGAGTGAGCAGGAAGAGGAGCTTGAGGATGGCCCTACTAT
AGCAAAGACTATCAAGACCTGGAAACAGTAGTGCGGTCTTTTCAGGATGACGTTGTCCTGAAGACAAGCCTGGATATTGG
AAGAAACAAAGTGGAAGATGCATTCTGCAAGGGTGAATTCAGGCTGAATGGGGAAAAATTATGGAAGAAAAGCAGAATGG
TCAAAGTGGGAGATACATTGGATCTTCTCATTGGAGAGGATAAGGAAGCAGGAACAGAGACAGTGATGCAGATTCTCCCG
AAAAAAAGTGTTTGAAGAGAAGACTGAAAGTGAAAAATACACAGTGGTGTTACAGCAGTGGAAAAACTTAAAAATGCCTA
AGAAGAGAATGTCTAAA

Alignment

ORF - retro_pabe_2922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.14 %
• Parental protein coverage: 57.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DEEDSDEESDYDEMSEQEEELEDDPTVVK-NYKDLEKAVQSFRYDVILKTGLDIGRNKVEDAFYKGELRL
          DEEDSD.ESD..EMSEQEEELED.PT..K..Y.DLE..V.SF..DV.LKT.LDIGRNKVEDAF.KGE.RL
Retrocopy DEEDSDAESDQNEMSEQEEELEDGPTIAK<DYQDLETVVRSFQDDVVLKTSLDIGRNKVEDAFCKGEFRL

Parental  NEEKLWKKSRTVKVGDTLDLLIGEDKEAGTETVMRIL-LKKVFEEKTESEKYRVVLRRWKSLKLPKKRMS
          N.EKLWKKSR.VKVGDTLDLLIGEDKEAGTETVM.IL..KKVFEEKTESEKY.VVL..WK.LK.PKKRMS
Retrocopy NGEKLWKKSRMVKVGDTLDLLIGEDKEAGTETVMQIL>RKKVFEEKTESEKYTVVLQQWKNLKMPKKRMS

Parental  K
          K
Retrocopy K

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	13.27 RPM
SRP007412_cerebellum	0.00 RPM	16.66 RPM
SRP007412_heart	0.00 RPM	17.64 RPM
SRP007412_kidney	0.03 RPM	26.05 RPM
SRP007412_liver	0.00 RPM	15.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2922 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2922 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003732	1 retrocopy	retro_cfam_1818,
Homo sapiens	ENSG00000130349	1 retrocopy	retro_hsap_3538,
Gorilla gorilla	ENSGGOG00000006113	1 retrocopy	retro_ggor_2389,
Macropus eugenii	ENSMEUG00000013534	1 retrocopy	retro_meug_2181,
Microcebus murinus	ENSMICG00000004137	1 retrocopy	retro_mmur_1269,
Macaca mulatta	ENSMMUG00000007391	1 retrocopy	retro_mmul_115,
Nomascus leucogenys	ENSNLEG00000013450	2 retrocopies	retro_nleu_1433, retro_nleu_499,
Otolemur garnettii	ENSOGAG00000008839	2 retrocopies	retro_ogar_1396, retro_ogar_390,
Pongo abelii	ENSPPYG00000016885	1 retrocopy	retro_pabe_2922 ,
Pan troglodytes	ENSPTRG00000018464	2 retrocopies	retro_ptro_1453, retro_ptro_2405,
Tursiops truncatus	ENSTTRG00000008837	2 retrocopies	retro_ttru_324, retro_ttru_432,