Gene detail

Detail information of GWHGAAZE016665

Functional Annotation

Database	Orthologs	E value	Annotation
Nr	CDP08394.1	1.40517E-88	unnamed protein product [Coffea canephora]
Swissprot	tr\|Q43582\|LSM4_TOBAC	2E-13	Probable U6 snRNA-associated Sm-like protein LSm4
trEMBL	tr\|A0A068UJI5\|A0A068UJI5_COFCA	5E-89	Coffea canephora DH200=94 genomic scaffold, scaffold_32 {ECO:0000313\|EMBL:CDP08394.1}
TAIR10	AT1G20580.1	5E-50	Small nuclear ribonucleoprotein family protein

Location And Transcript Sequence (JBrowse)

Scaffold	Type	Start	End	Strand
GWHAAZE00000004	gene	80547650	80550771	+
GWHAAZE00000004	mRNA	80547650	80550771	+
GWHAAZE00000004	exon	80547650	80547808	+
GWHAAZE00000004	exon	80549519	80549571	+
GWHAAZE00000004	exon	80549648	80549714	+
GWHAAZE00000004	exon	80549801	80549857	+
GWHAAZE00000004	exon	80550540	80550771	+
GWHAAZE00000004	CDS	80547650	80547808	+
GWHAAZE00000004	CDS	80549519	80549571	+
GWHAAZE00000004	CDS	80549648	80549714	+
GWHAAZE00000004	CDS	80549801	80549857	+
GWHAAZE00000004	CDS	80550540	80550602	+
GWHAAZE00000004	three_prime_UTR	80550603	80550771	+

Transcript Sequence
>GWHTAAZE016685 ATGAGCAGAAGTTTGGGGATACCGGTAAAGCTACTGCACGAGGCAGCGGGTCACGTGGTGACCGTAGAACTGAAGAGTGGAGAGCTTTACAGAGGAAGTATGATTGAGTGCGAAGACAACTGGAATTGCCAACTCGAAAACATCACCTTCACCGCCAAGGATGGGAAGGTCTCACAACTCGAGCATGTTTTTATCCGAGGCAGCAAAGTTAGGTTTATGGTGATTCCAGACATGCTTAAGAATGCTCCAATGTTCAAGCGCCTAGAATCTAGAATCAAGGGCAAGGGCTCATCACTGGGTGTTGGCCGGGGTCGTGCAGTTGCAATGCGTGCTAGAGCTCAGGCTGCTGGTCGTGGAGCTCCTCCTGGTAGGGGTGCTGTGCCCCCTGTACGGAGGTAAAATATAATGCTCAGAACCTGGGGTGCTGTGGCCCCTGAAGCTCATATCTTGGTTACAAACTTTTTCGCCCGAGCATTTACATTATCTAGATCCCTGATTTTGTAACCTAAGAAAATAGAAGTTTGTGCAAGACAATTGGAATACTTTCATTTTGTAGTACGAATTAAGT

Network for GWHGAAZE016665

Network category	Network	Top300 PCC genelist
Coexpression Positive	Network	Top300 PCC genelist
Coexpression Negative	Network	Top300 PCC genelist

Functional Module

Module ID	Function Annotation

Protein Structure

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF01423.23	LSM	11	74	2.30E-15

Protein Sequence

Gene family

Gene family	subfamily
--	--

KEGG pathway

KO	Enzyme	pathway	mapID
K11088	SNRPD3, SMD3	Spliceosome	map03040
K11088	SNRPD3, SMD3	Mitophagy - yeast	map04139

Gene Ontology

GO term	Ontology	Name
GO:0000387	biological_process	spliceosomal snRNP assembly
GO:0005681	cellular_component	spliceosomal complex

Expression pattern

Expression pattern detail

SRP	Sample	Description	TPM
SRP075780	SRR3591705	youngest leaf	56.254
	SRR3591706	second leaf	35.808
	SRR3591707	mature leaf	21.155
	SRR3591708	Shoot apex	109.193
	SRR3591709	Stem	41.441
	SRR3591710	White floral bud	48.691
	SRR3591711	White flower	72.569
	SRR3591712	Green floral bud	66.347
	SRR3591713	Yellow flower	57.913
SRP173429	SRR8316895	Juvenile bud stage	54.874
	SRR8316896	Juvenile bud stage	73.081
	SRR8316897	Juvenile bud stage	37.487
	SRR8316894	Third green stage	25.340
	SRR8316900	Third green stage	84.931
	SRR8316901	Third green stage	89.024
	SRR8316898	Complete white stage	27.477
	SRR8316899	Complete white stage	87.557
	SRR8316903	Complete white stage	44.594
	SRR8316902	Silver flowering stage	32.986
	SRR8316904	Silver flowering stage	31.581
	SRR8316905	Silver flowering stage	17.527
	SRR8316906	Gold flowering stage	64.704
	SRR8316907	Gold flowering stage	80.447
	SRR8316908	Gold flowering stage	64.752
SRP132670	SRR6706286	Control	59.189
	SRR6706287	Light intensity 50%	57.638
	SRR6706288	Light intensity 20%	63.710
CNP0000432	CNS0095592	Slightly white alabastrum(diploid) 1	125.258
	CNS0095593	Slightly white alabastrum(diploid) 2	146.604
	CNS0095594	Slightly white alabastrum(diploid) 3	131.570
	CNS0095595	Whole white alabastrum(diploid) 2	96.642
	CNS0095596	Whole white alabastrum(diploid) 3	106.441
	CNS0095597	Whole white alabastrum(diploid) 4	81.873
	CNS0095598	Silvery flower (diploied) 1	90.593
	CNS0095599	Silvery flower (diploied) 2	80.649
	CNS0095600	Silvery flower (diploied) 3	61.005
	CNS0095601	Golden flower (diploid) 1	66.492
	CNS0095602	Golden flower (diploid) 2	50.815
	CNS0095603	Golden flower (diploid) 3	49.037
	CNS0095604	Slightly white alabastrum(tetraploid) 1	92.566
	CNS0095605	Slightly white alabastrum(tetraploid) 2	99.232
	CNS0095606	Slightly white alabastrum(tetraploid) 3	117.414
	CNS0095607	Whole white alabastrum(tetraploid) 1	54.300
	CNS0095608	Whole white alabastrum(tetraploid) 2	56.834
	CNS0095609	Whole white alabastrum(tetraploid) 3	76.340
	CNS0095610	Silvery flower (tetraploid) 1	82.886
	CNS0095611	Silvery flower (tetraploid) 2	60.757
	CNS0095612	Silvery flower (tetraploid) 3	48.175
	CNS0095613	Golden flower (tetraploid) 1	74.209
	CNS0095614	Golden flower (tetraploid) 2	79.760
	CNS0095615	Golden flower (tetraploid) 3	32.272
CRA001975	CRR073297	Stem 1	59.942
	CRR073298	Stem 2	57.782
	CRR073299	Stem 3	65.736
	CRR073300	Leaf 1	54.554
	CRR073301	Leaf 2	54.318
	CRR073302	Leaf 3	64.932
	CRR073303	Juvenile bud 1	56.564
	CRR073304	Juvenile bud 2	45.541
	CRR073305	Juvenile bud 3	36.038
	CRR073306	Third green 1	15.401
	CRR073307	Third green 2	14.829
	CRR073308	Third green 3	18.461
	CRR073309	Second white 1	16.236
	CRR073310	Second white 2	19.663
	CRR073311	Second white 3	14.816
	CRR073312	Silver flowering 1	14.930
	CRR073313	Silver flowering 2	14.147
	CRR073314	Silver flowering 3	11.850
	CRR073315	Gold flowering 1	27.835
	CRR073316	Gold flowering 2	36.130
	CRR073317	Gold flowering 3	22.651
	CRR073318	Tawny withering 1	54.230
	CRR073319	Tawny withering 2	61.702
	CRR073320	Tawny withering 3	60.934