ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTGCCAGATGCCGAGTCGCGCTTCCATGTCCTCGCGGTGGACGACAGCCTCGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattccgtccgtgtttctgggtgttttttttttctctccccttctttccctgcggcgaaattccgtctcatcatcatccgccgcgccctcgttgtccag

Basic information

species	Zea mays
transcript	GRMZM2G156019_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G156019_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g72330.1 (Oryza sativa), 5'ss of exon 1

GTGCCAGATGCCGAGTCGCGCTTCCATGTCCTCGCGGTGGACGACAGCCTCGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaa----------------ttccgtccgtgtttctgggtgttttttttttctctccccttctttccctgcggcgaaattccgtctcatcatcatccgccgcgccctcgttgtccag---------------
|||   ||||| |||||||| |||||||||||||||||||| || |||||  |||||||||| |||||||||||||||||||||| ||||||||||||||||||                  |   | || ||  | ||||||   | ||| | | |    |||  |   ||    |   ||   | |  ||||          |   ||  ||                    
GTGGTTGATGCGGAGTCGCGGTTCCATGTCCTCGCGGTGGATGATAGCCTGATCGACAGGAAGCTCATCGAGATGCTGCTCAAGAACTCGTCCTACCAAGgtgagtgcgtgaaaaatgatgttcttgaccttggatttgggtgggatgtttgtgttttgtgttcaatgtttggtttgttttttttttttctcatttcttcttctgaattctctgcttgcttgctactggtgcag

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|91048093|gb|EB158511.1|EB158511

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|91049479|gb|EB159897.1|EB159897

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|211439400|gb|FL402881.1|FL402881

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|148975637|gb|EE025768.2|EE025768

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|89759374|gb|DY688232.1|DY688232

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|148971158|gb|EE022012.2|EE022012

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|149112392|gb|EE295266.2|EE295266

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|76281690|gb|DV021258.1|DV021258

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|149096713|gb|EE182486.2|EE182486

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|211215269|gb|FL414788.1|FL414788

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|211097795|gb|FL409141.1|FL409141

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

EST: gi|91871779|gb|EB401736.1|EB401736

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTTCGGGGAGCAA
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGG-AGCAA

EST: gi|211324213|gb|FL425817.1|FL425817

EST:     CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAG                         TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG
genomic: CGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 30

GTGCCAGATGCCGAGTCGCGCTTCCATGTCCTCGCGGTGGACGACAGCCTCGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattcc ... cgttgtccagTGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 33

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCAGATGCCGAGTCGCGCTTCCATGTCCTCGCGGTGGACGACAGCCTCGTCGACAGGAAACTCATCGAGATGCTGCTCAAGACCTCGTCCTACCAAGgtgaaattccgtccgtgtttctgggtgttttttttttctctccccttctttccctgcggcgaaattccgtctcatcatcatccgccgcgccctcgttgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT