RetrogeneDB ID: retro_ptro_3186

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:17031831..17032427(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35C2
• Ensembl ID: ENSPTRG00000013582
• Aliases: None
• Description: None

Sequence

>retro_ptro_3186
TTCACAATAACCAAATCTTTAGCTGTCCTCTTCATCATCAATCTTCTCTCTGATCTCCAAGCTGGAGGAGCTGCAATGAC
ACTGGTCCTTGTGATCCTCCTCATCGCCGGGGGTCTCTTCATGTTCACCTTCAAGTCCACACAGCCCAATGTGGAGGGCT
TTGCCTTGGTGCTGGGGACCTTGCTCATTGGTGGCATTCGCTGAACCCTCACCCGGACATTCCTGCAGAAGGCTGATCTT
GGCTTCCAGGATTCCATCGACAGCATGTTCCACCTGCAGCCACTCACGTTTCTGGGGCTTTTCCCTCTCTTTGCTGTATG
TGAAAGTCGCCATTTGTCCATGTGTGGGGAAATATTTCATTTCCAGGATACAGGGCTGCTCCTGGGGTACTTGGGAGCCT
CTTCCTTGGTGGGCATCTCACCTTTGGTTTGGACTTCTCTGAGTTCATCCTGGTCTCCAGACCCTCCAGCCTCACTCTCT
CCATTGCTGGCGTTTGGAAGGAAGTGTGCACTTTGCTGTTGGCAGCTCATCTGCTGGGTGATCAGATCAGCCACCTGAAC
TGGCTGGGCTTCCTTCTCTGCCTCTCAGGAATATCC

Alignment

ORF - retro_ptro_3186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.72 %
• Parental protein coverage: 54.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTMTKSSAVLFIL-IFSLIFKLEELR-AALVLVVLLIAGGLFMFTYKSTQFNVEGFALVLGASFIGGIRW
          .T.TKS.AVLFI..IFSLI.KLEEL....LVLV.LLIAGGLFMFT.KSTQ.NVEGFALVLG...IGGIR.
Retrocopy FTITKSLAVLFII>IFSLISKLEELQ<MTLVLVILLIAGGLFMFTFKSTQPNVEGFALVLGTLLIGGIR*

Parental  TLTQMLLQKAELGLQNPIDTMFHLQPLMFLGLFPLFAVFEGLHLSTSEKIFRFQDTGLLL-RVLGSLFLG
          TLT...LQKA.LG.Q..ID.MFHLQPL.FLGLFPLFAV.E..HLS....IF.FQDTGLLL..VLGSLFLG
Retrocopy TLTRTFLQKADLGFQDSIDSMFHLQPLTFLGLFPLFAVCESRHLSMCGEIFHFQDTGLLL<GVLGSLFLG

Parental  GILAFGLGFSEFLLVSRTSSLTLSIAGIFKEVCTLLLAAHLLGDQISLLNWLGFALCLSGIS
          G.L.FGL.FSEF.LVSR.SSLTLSIAG..KEVCTLLLAAHLLGDQIS.LNWLGF.LCLSGIS
Retrocopy GHLTFGLDFSEFILVSRPSSLTLSIAGVWKEVCTLLLAAHLLGDQISHLNWLGFLLCLSGIS

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	32.05 RPM
SRP007412_cerebellum	0.00 RPM	30.01 RPM
SRP007412_heart	0.00 RPM	8.60 RPM
SRP007412_kidney	0.00 RPM	40.43 RPM
SRP007412_liver	0.00 RPM	49.26 RPM
SRP007412_testis	0.00 RPM	16.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3186 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3186 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4789
Gorilla gorilla	retro_ggor_2982
Pongo abelii	retro_pabe_3726

---

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,