RetrogeneDB ID: retro_pabe_3726

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:16852183..16852779(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35C2
• Ensembl ID: ENSPPYG00000011091
• Aliases: None
• Description: solute carrier family 35 (GDP-fucose transporter), member C2 [Source:HGNC Symbol;Acc:17117]

Sequence

>retro_pabe_3726
TTCACAATAACCAAATCTTTAGCTGTCCTCTTCATCGTCAATCTTCTCTCTGATCTCCAAGCTGGAGAAGCTGCAATGGC
ACTGATCCTTGTGATCCTCCTCATCACCAGGGGTCTCTTCATCTTCACCTTCAAGTCCACACAGCCCAATGTGGAGGGCT
TCGCCTTGGTGCTGGAGACCTTGCTCATTGGTGGAATTCGCTGAACCCTCACCCGGACATTCCTGCAGAAGGCTGATCTT
GGCTTCCAGGACTCCATCGACAGTACGTTCCACCTGCAGCCACTCACGTTTCTGGGGCTTTTCCCTCTCTTTGCTGTATG
TGAAAGTTGCCATTTGTCCACATCTGGGGAAATATTTCATTTCCAGGATACAGGGCTGCTCCTGGGGTACTTGGGAGCCT
CTTCCTTGGTGGGCGTCTCACCTTTGGTTTGGACTTCTCTGAGTTCCTCCTGGTCTCCAGACCCTCCAGCCTCACTCTCT
CCATTGCTGGCATTTGGAAGGAAGTCTGCACTTTGCTGTTGGTAGCTCATCTGCTGGGTGATCAGATCAGCCACCTGAAC
TGGCTGGGCTTCCTTCTCTGCCTCTTGGGAATATCC

Alignment

ORF - retro_pabe_3726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 58.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTMTKSSAVLFIL-IFSLIFKLEELR-AALVLVVLLIAGGLFMFTYKSTQFNMEGFALVLGASFIGGIRW
          .T.TKS.AVLFI..IFSLI.KLE.L...AL.LV.LLI..GLF.FT.KSTQ.N.EGFALVL....IGGIR.
Retrocopy FTITKSLAVLFIV>IFSLISKLEKLQ<MALILVILLITRGLFIFTFKSTQPNVEGFALVLETLLIGGIR*

Parental  TLTQMLLQKAELGLQNPIDTMFHLQPLMFLGLFPLFAIFEGLHLSTSEKIFRFQDTGLLL-RVLGSLFLG
          TLT...LQKA.LG.Q..ID..FHLQPL.FLGLFPLFA..E..HLSTS..IF.FQDTGLLL..VLGSLFLG
Retrocopy TLTRTFLQKADLGFQDSIDSTFHLQPLTFLGLFPLFAVCESCHLSTSGEIFHFQDTGLLL<GVLGSLFLG

Parental  GILAFGLGFSEFLLVSRTSSLTLSIAGIFKEVCTLLLAAHLLGDQISLLNWLGFALCLSGIS
          G.L.FGL.FSEFLLVSR.SSLTLSIAGI.KEVCTLLL.AHLLGDQIS.LNWLGF.LCL.GIS
Retrocopy GRLTFGLDFSEFLLVSRPSSLTLSIAGIWKEVCTLLLVAHLLGDQISHLNWLGFLLCLLGIS

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	22.17 RPM
SRP007412_cerebellum	0.00 RPM	27.00 RPM
SRP007412_heart	0.03 RPM	7.01 RPM
SRP007412_kidney	0.00 RPM	27.98 RPM
SRP007412_liver	0.00 RPM	17.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3726 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3726 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4789
Pan troglodytes	retro_ptro_3186
Gorilla gorilla	retro_ggor_2982

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011583	2 retrocopies	retro_chof_2686, retro_chof_952,
Callithrix jacchus	ENSCJAG00000017091	1 retrocopy	retro_cjac_4140,
Homo sapiens	ENSG00000080189	1 retrocopy	retro_hsap_4789,
Gorilla gorilla	ENSGGOG00000014052	1 retrocopy	retro_ggor_2982,
Nomascus leucogenys	ENSNLEG00000006880	1 retrocopy	retro_nleu_1104,
Pongo abelii	ENSPPYG00000011091	1 retrocopy	retro_pabe_3726 ,
Pan troglodytes	ENSPTRG00000013582	1 retrocopy	retro_ptro_3186,
Tupaia belangeri	ENSTBEG00000005486	1 retrocopy	retro_tbel_531,