ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatgatatggcaccgacagtttaaattttcagttaatacctggttcttgtaaaaaccactagcctgcaggaaaagttatgtatctcattttcttcacacag

Basic information

species	Zea mays
transcript	GRMZM2G105539_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G105539_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 5'ss of exon 9

TTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatgatatggcaccgacagtttaaattttcagttaatacctggttcttgtaaaaaccactagcctgcaggaaaagttatgtatctcattttcttcacacag
|||  |   ||| ||||||||||| || | |||||||||||| |||||| |||| ||||||||  |||| ||||||||||||||| ||||||||||||||||| |  | |||     |||| |   | | | |  ||| | |  ||| | |||||| ||||        ||||||   | |||   ||||  |||  | ||     
TTCCCTAAGAAATGAAAGTGTTCCCGTTAAGAGACTCATTGTTAACCAAATTCTACCACCTTCGTCATCAGACTGTAAATTCTGTGCTATAAAAAGAAAGgtagagttcataatctgccgaaa---tgattctctagtaattgtctgctgcttgtagaaactgtg---ttgcagggccatttac-catcttctttcatccag----

upper sequence: GRMZM2G105539_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA20G32200.1 (Glycine max), 5'ss of exon 10

TTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtac---aaatgatatggcaccgacagtt---taaattttcagttaatacctggttcttgtaaaaaccactagcctgcaggaaaagttatgtatctcattttcttcacacag
|||  || | ||||||| ||||||||| | |||||| ||||| |||||  |||| ||||| || ||||| || || || || ||| |||| |||||||||||||   || || | |  |    |   ||   |  ||| |   | | |   |   | |  |  ||  || |    || |   | || |  | ||  ||              
TTCCCTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCATCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAGgtactttaattgttttctcttttatttttgcatggattgtatctgagtggttaactataatgtaattcatt---ttgaactgatagctgagcataccaaacaa---------

upper sequence: GRMZM2G105539_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G35320.2 (Glycine max), 5'ss of exon 10

TTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatgatatggcaccgacagtttaaattttc---agttaatacctggttcttgtaaa-aaccact--------agcctgcaggaaaagttatgtatctcattttcttcacacag--------------------------------------------------
||| ||| | ||||||| ||||||||| | |||||| ||||| |||||  |||| ||||| || ||||| || || || || ||| |||| |||||||||||||      | |     |   | || | || |     |  | ||| |||    |   ||| ||  |||        |    | || |||| |  ||| |||  |    |     ||                                                   
TTCCTTGAAGAAGGAAAATGTTCCTGTGAAGAGACTTATTGTCAACCAGATTCTTCCACCGTCTACATCTGATTGCAAGTTTTGTGCTATGAAAAGAAAGgtactttaattgttttctctttaattgatatgtaacagaactgatagctgagcataccaaagaagaacttgaaggagaaggggaagaaaaactcttgtgtcttgtacgttatgttcatttttatttaaagagctaaaacttgcaataccatgaacaaacttttttcag

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|211018633|gb|FL458034.1|FL458034

EST:     CTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: CTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|87153613|gb|DY398402.1|DY398402

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAA-GAAAG                         GATCAAACGCGTGCATTGGATATGATACCGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|6973389|gb|AW438083.1|AW438083

EST:     TTCTGCCACCTTCAACATCGGACTGTACATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGCATATGATACGGACTGAC
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGAC

EST: gi|5762109|gb|AI967157.1|AI967157

EST:     TTCTGCC-CCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|6031284|gb|AW076291.1|AW076291

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|5296253|gb|AI782933.1|AI782933

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAA
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAA

EST: gi|78022914|gb|DV491301.1|DV491301

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|87152689|gb|DY397478.1|DY397478

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|40336422|gb|CK370492.1|CK370492

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

EST: gi|33097578|gb|CF057538.1|CF057538

EST:     TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAG                         GATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT
genomic: TTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 21

TTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatga ... cttcacacagGATCAAACGCGTGCATTGGATATGATACGGACTGACCCAGAGTTAAAAGGTTTGAACATTATCCAAGCACCTCTTGTGGACATGGAGATTAGAGGTGTTC

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 32

Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 15

Block sizes: 38 (upstream exon), 45 (downstream exon)
Score: 14

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGTTGCAAAAGGAAAGTGTTCCTGTAAGGAGACTCATTGTGAACCAAGTTCTGCCACCTTCAACATCGGACTGTAAATTCTGTTCTATAAAAAGAAAGgtacaaatgatatggcaccgacagtttaaattttcagttaatacctggttcttgtaaaaaccactagcctgcaggaaaagttatgtatctcattttcttcacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA