ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTGCCGGCGCGAGGGTCCTGTTCTATCCGACGCTTCTCTACAACGTGCTCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatcttttgcttgtctccatgtttatgtcctggtttcgttatttctgatccggggtgcgatttggagatatgcttttggggacgtccagtgttgt...

Basic information

species	Zea mays
transcript	GRMZM2G031435_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G031435_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g44910.1 (Oryza sativa), 5'ss of exon 1

TGGTGCCGGCGCGAGGGTCCTGTTCTATCCGACGCTTCTCTACAACGTGCTCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgc--tgatcttttgcttgtctccatgtttatgtcctg-gtttcgttatttc----tgatccggggtgcgatttggagatatgctt-ttggggacgtccagtgttgt
 || |||||||||||||| |||||||| |||||||| ||||||||||| |||||||||||||||||    |||||||| |||||||||||||||||| |||||   | |||||   ||  ||||  |    || | |||    | ||  ||       |||  || |    | ||  |   |||  | |||||||||  |        
CGGCGCCGGCGCGAGGGTGCTGTTCTACCCGACGCTGCTCTACAACGTCCTCCGCAACCGGTTCGAGTCTGAGTTCCGGTGGTGGGATCGCATCGACCAGgtgtgttaatcttaccctcatctctctcccaatatactgcaccttgtcgttctggagcgatttggtgctttaatttcactcatggatattggggacgatc--------

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|88753204|gb|DY537345.1|DY537345

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211119234|gb|FL049569.1|FL049569

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGT
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGT

EST: gi|211118449|gb|FL049565.1|FL049565

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACNAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|71441815|gb|DR822865.1|DR822865

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211118444|gb|FL049560.1|FL049560

EST:     TCCGCAACCGGTTCCATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|148970664|gb|EE021375.2|EE021375

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211118452|gb|FL049568.1|FL049568

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCCTGAA
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCC-TGAA

EST: gi|93284231|gb|EB676495.1|EB676495

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|91873023|gb|EB402980.1|EB402980

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211118448|gb|FL049564.1|FL049564

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|26559099|gb|CA831334.1|CA831334

EST:     CGCAACCGGTTCGATGGCGAGTTCCCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: CGCAACCGGTTCGATGGCGAGTTCC--GCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211119235|gb|FL049570.1|FL049570

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|71448351|gb|DR829401.1|DR829401

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|71439137|gb|DR820187.1|DR820187

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211118438|gb|FL049554.1|FL049554

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCG

EST: gi|211118445|gb|FL049561.1|FL049561

EST:     TCCGCAACCGGTTCCATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211119237|gb|FL049572.1|FL049572

EST:     CCGCAACCGGTTCGATNGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTTCTGTTCCGTKCTCTAGCGATGTTCTGCGCCTGAAG
genomic: CCGCAACCGGTTCGAT-GGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|88746187|gb|DY530328.1|DY530328

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|71766612|gb|DR964549.1|DR964549

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|78103952|gb|DV522370.1|DV522370

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|22549089|gb|BU101290.1|BU101290

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|71430075|gb|DR811125.1|DR811125

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|76288945|gb|DV028513.1|DV028513

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|211118447|gb|FL049563.1|FL049563

EST:     CCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGGACAAG                         TATGTTYTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCG
genomic: CCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCG-ACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCG

EST: gi|211118451|gb|FL049567.1|FL049567

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|76280780|gb|DV020348.1|DV020348

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|76928948|gb|DV171821.1|DV171821

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|74232090|gb|DT640004.1|DT640004

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

EST: gi|101383931|gb|EB814020.1|EB814020

EST:     TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAG                         TATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG
genomic: TCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAG

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: 42 (upstream exon), 47 (downstream exon)
Score: 16

TGGTGCCGGCGCGAGGGTCCTGTTCTATCCGACGCTTCTCTACAACGTGCTCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatct ... ctatcttcagTATGTTTTGCTAGGTGCTGTTCCGTTCTCTAGCGATGTTCTGCGCCTGAAGCAACTTGGTGTAAGAGGAGTTGTTACACTCAATGAACCCTATGAAACTC

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 47

Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 26

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 66

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGCCGGCGCGAGGGTCCTGTTCTATCCGACGCTTCTCTACAACGTGCTCCGCAACCGGTTCGATGGCGAGTTCCGCTGGTGGGATCGCATCGACAAGgtgctgatcttttgcttgtctccatgtttatgtcctggtttcgttatttctgatccggggtgcgatttggagatatgcttttggggacgtccagtgttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG