ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGCTTGCCAACCCTAATGCACCTCTTGGTTACACATTGTGCTTCCTCAACTTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagattctccctatcttataccaagctatcatgaaacattatgatcattattctaaatagaagaaatgtttgatgtag

Basic information

species	Zea mays
transcript	GRMZM2G176029_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g39260.1 (Oryza sativa), 5'ss of exon 6

AGCTTGCCAACCCTAATGCACCTCTTGGTTACACATTGTGCTTCCTCAACTTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagattctccctatcttataccaagctatcatg-aaacattatgatcattat-tctaaatagaa-gaaatgtt-tgatgtag---
||||||| ||||||||||| ||||| || ||||||||||||||||||||||||||||||||||| || || || |||||||||||||| |||||||| |||||| || |  ||  | ||   |||  ||   ||  || |||  |||| ||| |  | |||| || ||| | |||||  || | | |   
AGCTTGCTAACCCTAATGCGCCTCTGGGCTACACATTGTGCTTCCTCAACTTAGCTTTTGATGGTTACACCAATTCGACCCAAGATTTGATAAAGTCTAGgtaactacaccctgtccattccatattaaagcattctggaaattttatcatcttcttatctacatggaaagtaatgtcgtgttattgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|78118465|gb|DV536850.1|DV536850

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|148931883|gb|EC877348.2|EC877348

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCCAGATTTAATAAAGTCAAG                         GTACCCAAAAACCAACCCCTGGGAAATAATGCTTGGCATGAACC
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACC

EST: gi|50335103|gb|CO530229.1|CO530229

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|78080957|gb|DV509369.1|DV509369

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|33466642|gb|CF243691.1|CF243691

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|148985614|gb|EE029715.2|EE029715

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCCATGG-ATATAATGCTCGGCATTGA-CCTCTGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCC-ATGGGATATAATGCTTGGCAT-GAACCTCTGG

EST: gi|110521911|gb|EE026095.1|EE026095

EST:     TTAGCTTTTGAGGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|78107091|gb|DV525509.1|DV525509

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|149005382|gb|EE039934.2|EE039934

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|78080956|gb|DV509368.1|DV509368

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|50324993|gb|CO520119.1|CO520119

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|74234865|gb|DT642779.1|DT642779

EST:     TTAGCTTTTGATGGATATACTAACTCGACTCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|148953372|gb|EE152866.2|EE152866

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCT
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCT

EST: gi|71318367|gb|DR795945.1|DR795945

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|50335104|gb|CO530230.1|CO530230

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

EST: gi|78107092|gb|DV525510.1|DV525510

EST:     TAGCTTTTTGATGGATATACTAACTCGACCCCAGATTTAATAAAGTCAAG                         GTACCCAAAAACA
genomic: TAGCTTTT-GATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACA

EST: gi|71318369|gb|DR795946.1|DR795946

EST:     TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAG                         GTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG
genomic: TTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

AGCTTGCCAACCCTAATGCACCTCTTGGTTACACATTGTGCTTCCTCAACTTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagat ... tttgatgtagGTACCCAAAAACAAACCCATGGGATATAATGCTTGGCATGAACCTCTGGGGGACCATATATAATGCTGTAATTATGTTTGTTGCGCCATTACTATTCAGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTTGCCAACCCTAATGCACCTCTTGGTTACACATTGTGCTTCCTCAACTTAGCTTTTGATGGATATACTAACTCGACCCAAGATTTAATAAAGTCAAGgtaattagattctccctatcttataccaagctatcatgaaacattatgatcattattctaaatagaagaaatgtttgatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA