ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca...

Basic information

species	Zea mays
transcript	GRMZM2G026969_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g66940.1 (Oryza sativa), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaa--gccg---ccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca
||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||   || |||||||||||||| |||||||  ||||||||| |    || |    |||   ||   ||  | | ||  |    || | ||   | ||  |   ||  | | ||  |     || ||||||  | |      
CCTCCGCGCCGACGGGGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACCCACGCCGAGCTCAACGTCGAGCTCATCAAGAGGgtaagccccccgctgatctccttatcccccctccgtgttcttctcatctccgcgatctgcggaggaggcagttccgtt-ccacccgatcccgtcgcgcgcg----

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G41960.2 (Glycine max), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaag----tcaagccgccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca
||| ||||||||||| ||||| ||||||||||||||| | |||||||||||||||||||||||||   |||| || |||||  |||  |||||| |    ||| |    |    || | ||   | ||    |   ||       | || || |||              | |  |   ||| |      || |  |       
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACAGAAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAATCTCGAACTCATCAGATCTgtatgcatcttttccctctcttaactttctcggaaaatttttaaccttttccctgaaaacgaagtctttgttccatgtatgagttgagatgtgtgatctg----

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G03430.1 (Glycine max), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca-------
||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||   |||| || |||||| | |  |||||| |    ||| |      |  | |  ||||  ||   || || |  | | ||| ||  |       |      | | | ||      | |   || | |||    ||       
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACCGGAACCCCAGCGCCGACATGCTCCTCAAGCCCGAAGAACTCAACCTTGAACTCATCAGATCTgtatg------catcttttccctctctct-cgctctctctactttctcggaaaatatttaaccttttcccggaaaacgaagtctttgtttcgtgattccatgtatga

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G13580.1 (Glycine max), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgccct---ggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca
||| ||||||||||| ||||| ||||||||||||||| | ||||||||||||||||||||||||||  |||| || |||||  |||  |||||| |    ||| |  || |     |       ||    |  |  | |  ||   ||  | |  |  | |        |         |  ||     |  |  ||      
CCTACGCGCCGACGGAGAGCGTGAGTTCATGTTCTACAGAAACCCCAGCGCCGACATGCTCCTCACGCCCGAAGATCTCAATCTCGAACTCATCAGATCTgtacgcaaatctattttctcaattctcaactttcagttcttgtcgtttttcttcgttagtgtttg--tgtttcacgcgcgtgtggtaatggattatgctgag-

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G05580.1 (Glycine max), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca-----
||| ||||||||||| ||||| ||||||||||||||| | |||||||| |||||||||||||||||  |||| || |||||  |||  |||||| |    |||||  || |   |      ||    |  |  | |   | | ||    |  |||      ||   || |||   || || || | || | |             
CCTACGCGCCGACGGGGAGCGTGAGTTCATGTTCTACAGAAACCCCAGTGCCGACATGCTCCTCACGCCCGAAGATCTCAATCTCGAACTCATCAGATCCgtaagcaaatctatctcaattctcaactttcagttcttctccttttttct--tcctttcttagt--tagtgtttgtgtttcacgc-gtgtggaaatgatgggctt

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT3G59480.1 (Arabidopsis thaliana), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccg--ccctggcccttgcttggcg-atccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca--------------------------------------------------------------------------
 ||  |  | || || || || ||||||||||||||||| ||||| || ||||| |||||||||  | |||||||||||||  | |   ||||| |    ||| || |          |      |   || |   |   |      |    ||   |   | |   |||    | |  ||  |   |    |  |    | |                                                                          
ACTAAGATCTGATGGAGAACGTGAGTTCATGTTCTACCGGAACCCTAGTGCCGATATGCTCCTCCGTCCCGACGAGCTCAATCTTGATGTCATCAGATCTgtacgttatttttatttttaattaatatatgacacgtaggcaaattcttttttgggtccgtgtctcacatttaattagcgaacggtgctacatcattaacgtaacggttgttggtatacgtaacgtagatgtcaagttaggttaatgagtgctctgttttgtttttgttttacacag

upper sequence: GRMZM2G026969_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv05s0102g00710.t01 (Vitis vinifera), 5'ss of exon 1

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgcc--ctggcccttgcttggcga--tccccgtgccttcccgt--gatccgcggacagccatactgtaactgattgaccccgtctagtggcagca
 || ||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||| || |   | || ||||||||| ||| |||||| ||    ||| ||     |  |  ||  | |||     ||||  || |  |   ||||| |  ||   | | | |  |     |    |   ||      |||  |       
GCTCCGCGCCGACGGAGAGCGTGAGTTCATGTTCTACCGGAACCCTAGCGCCGACATGCTGCTGAAGCCGGAGGAGCTCAACCTCGAGCTCATTCGATCCgtacgtttcttcttcttcttactcttctgctgcgaactctctctcttttccctttagaattgagaagattctcggagatcttccatggatttctctcttt------

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|211228023|gb|FK951197.1|FK951197

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCT
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCT

EST: gi|71426192|gb|DR807242.1|DR807242

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGAGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|211228018|gb|FK951192.1|FK951192

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GATGCGGACTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|71424817|gb|DR806448.1|DR806448

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|60394097|gb|DN226967.1|DN226967

EST:     ACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: ACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|71301234|gb|DR786653.1|DR786653

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|71772120|gb|DR970057.1|DR970057

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|91056053|gb|EB166471.1|EB166471

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|93014524|gb|EB640044.1|EB640044

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|211228020|gb|FK951194.1|FK951194

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTT
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTT

EST: gi|74244919|gb|DT652833.1|DT652833

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|74235495|gb|DT643409.1|DT643409

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|78112340|gb|DV530734.1|DV530734

EST:     CGACATGCTCCTCACTGCCGACGAGCTNCA-CGTCGGGCTCATCCGGAGG                         GGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCG
genomic: CGACATGCTCCTCACTGCCGACGAGCT-CAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagG-CTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCG

EST: gi|211228015|gb|FK951189.1|FK951189

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|78092755|gb|DV521129.1|DV521129

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|148990819|gb|EE032235.2|EE032235

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|71300724|gb|DR786400.1|DR786400

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|78078691|gb|DV507103.1|DV507103

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|9824982|gb|BE575184.1|BE575184

EST:     CGACATGCTCCTCACTGNCGACGAGCTCAACGTCGGGCTCATCCAGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCG
genomic: CGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCC-GGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCG

EST: gi|94479813|gb|EB708771.1|EB708771

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|71449386|gb|DR830436.1|DR830436

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|148951327|gb|EC897036.2|EC897036

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

EST: gi|60344909|gb|DN211882.1|DN211882

EST:     CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGG                         GCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG
genomic: CCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGG

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: 26

CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaag ... ttttctacagGCTGCGGTCTTTCACTACGGATCAATAAGCTTGATTGCTGAGCCTTGCCGGACAGCACATCTCCGTGCCATGGAAATTGCCAAAGAGGCTGGTGCACTGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 47

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 19

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCGCGCCGACGGCGAGCGCGAGTTCATGTTCTACCGCAACCCCAGCGCCGACATGCTCCTCACTGCCGACGAGCTCAACGTCGGGCTCATCCGGAGGgtaagtcaagccgccctggcccttgcttggcgatccccgtgccttcccgtgatccgcggacagccatactgtaactgattgaccccgtctagtggcagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccgtc