RetrogeneDB ID: retro_cjac_4140

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:15043395..15043987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35C2
• Ensembl ID: ENSCJAG00000017091
• Aliases: None
• Description: solute carrier family 35 (GDP-fucose transporter), member C2 [Source:HGNC Symbol;Acc:17117]

Sequence

>retro_cjac_4140
TTCACAATAACCAGATCTTCAACCATCCTCTTCATCTTCATCTTCTCTCTGCTCTCCAAGCTGGAGGAGGTGCAATGGCA
CTGGTCCTGGTGATTCTCCTCATCACCGGGGGTCTCTTCATGTTCACCTTCAAGTCCACACAGCCCAATGTGGAGGGCTT
CGCCTTGGTGCTGGGGACCTCGCTCATTGGTGGCATTCACTGAACGCTCACCCAGACGTTCCTGCAGAAGACTGATCTTG
GCCTCCAGGATGCCATCGACAGCGTGTTCCACCTGCAGCCACTCATGTTTCTGGGGTTCTTCCCTCTTCTTTGCTGTATA
TGAAAGCCTCCATTTGTCCACGTCTAAGAAAATCTTTCATTTCCAGGACACAGGGCTGCTCCTGGGGTACTTAGGAGCCT
CTTCCTTGGTGGGCTTCTCACATTTGGTTTGGGCTTCTCTGAGTTCCTCCTGGTCTCCAGACCCTCCAGCCTCACTCTCT
CCATTGCTGGCATTTGGAAGAAGTCTGCAGTTTGCTGTTGGCAGCTCATCTGGTGGGTGATCAGCTCAGCCACCTGAACT
GGCTGGGCTTCCTGCTCTGCCTCTCAGGAATA

Alignment

ORF - retro_cjac_4140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.73 %
• Parental protein coverage: 50.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YTMTKSSAVLFILIFSLIFKLEELR-AALVLVVLLIAGGLFMFTYKSTQFNVEGFALVLGASFIGGIRWT
          .T.T.SS..LFI.IFSL..KLEE....ALVLV.LLI.GGLFMFT.KSTQ.NVEGFALVLG.S.IGGI..T
Retrocopy FTITRSSTILFIFIFSLLSKLEEVQ<MALVLVILLITGGLFMFTFKSTQPNVEGFALVLGTSLIGGIH*T

Parental  LTQMLLQKAELGLQNPIDTMFHLQPLMFLGLFPL-FAVFEGLHLSTSEKIFRFQDTGLLLRVLG-SLFLG
          LTQ..LQK..LGLQ..ID..FHLQPLMFLG.FPL.FAV.E.LHLSTS.KIF.FQDTGLLL..LG.SLFLG
Retrocopy LTQTFLQKTDLGLQDAIDSVFHLQPLMFLGFFPL>FAVYESLHLSTSKKIFHFQDTGLLLGYLG<SLFLG

Parental  GILAFGLGFSEFLLVSRTSSLTLSIAGIFK-EVCTLLLAAHLLGDQISLLNWLGFALCLSGI
          G.L.FGLGFSEFLLVSR.SSLTLSIAGI.K.EVC.LLLAAHL.GDQ.S.LNWLGF.LCLSGI
Retrocopy GLLTFGLGFSEFLLVSRPSSLTLSIAGIWK<EVCSLLLAAHLVGDQLSHLNWLGFLLCLSGI

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
SRP051959_colon	0.00 RPM	10.67 RPM
SRP051959_heart	0.00 RPM	7.44 RPM
SRP051959_kidney	0.00 RPM	12.31 RPM
SRP051959_liver	0.00 RPM	5.65 RPM
SRP051959_lung	0.00 RPM	10.77 RPM
SRP051959_lymph_node	0.00 RPM	12.17 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.94 RPM
SRP051959_spleen	0.00 RPM	10.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4140 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4140 has 0 orthologous retrocopies within eutheria group .

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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,