ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGAGCAGAAGGTTGAGCCTGTGATTATGGATGAGAGCGTGATGAAGGCATGTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaacattccatctccttccttatttgtttaagaatccatgtgtcatattatttcttgtgctcatgctgcttcctttgttttttttcctaaatgaatgttgtttcttttgtag

Basic information

species	Zea mays
transcript	GRMZM2G046418_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G046418_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g61500.1 (Oryza sativa), 5'ss of exon 2

AGAGCAGAAGGTTGAGCCTGTGATTATGGATGAGAGCGTGATGAAGGCATGTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaacattccatctccttccttatttgtttaagaatccatgtgtcatattatttcttg-tgctcatgctgcttcctttgttttttttcctaaatgaatgttgtttcttttgtag
|||||||| ||  ||||| || ||||||||||||||| |||||||||| |||||||||||||  ||||| |||||||||||||| || || ||||| |||||||||||| | |   |||||  |||  |   || ||  ||  |    || | |||| ||||| |||| || | | ||   |||||||| |||    |  |                  
AGAGCAGAGGGCCGAGCCAGTAATTATGGATGAGAGCATGATGAAGGCTTGTGAGGCTGTTGGCCGTGTAAGAGCTGAAGTTGACAGACTCTCTGCCAAGgtgaaggaataatgtttctccagcctcttccatt-aaacattaac---tcttcttatatcttgatgctgatacggttt---ttgtttttgttctattaccag-----------------

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|28568924|gb|CB280799.1|CB280799

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|93012052|gb|EB637572.1|EB637572

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTTCTAAG                         GTGTGTGACTTGNAGAAGAATGTGCTTGCAGGGAGAAAAGTTGA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGA

EST: gi|148946348|gb|EC891654.2|EC891654

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|211392386|gb|FL034004.1|FL034004

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|71772733|gb|DR970660.1|DR970660

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAAAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|211395017|gb|FL034024.1|FL034024

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCANGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|148935823|gb|EC879869.2|EC879869

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|31354102|gb|CD438459.1|CD438459

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|149001144|gb|EE038406.2|EE038406

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAA

EST: gi|211395009|gb|FL034016.1|FL034016

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGCAGAAGAATGTGCTTGCAGGGAGAAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAA

EST: gi|149111411|gb|EE294913.2|EE294913

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|71325371|gb|DR799360.1|DR799360

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|29544381|gb|CB604761.1|CB604761

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|28987546|gb|CB351688.1|CB351688

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|93283293|gb|EB675557.1|EB675557

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|211397626|gb|FL034026.1|FL034026

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGA

EST: gi|149071588|gb|EE159980.2|EE159980

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|211395014|gb|FL034021.1|FL034021

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGNAGAAGAATGTGCTTGCAGGGAGAAAAAGT-GATGATAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAA-GTTGATGATAA

EST: gi|149111412|gb|EE294914.2|EE294914

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGNAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

EST: gi|211395003|gb|FL034010.1|FL034010

EST:     GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAG                         GTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA
genomic: GTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 64

AGAGCAGAAGGTTGAGCCTGTGATTATGGATGAGAGCGTGATGAAGGCATGTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaac ... tcttttgtagGTGTGTGACTTGGAGAAGAATGTGCTTGCAGGGAGAAAAGTTGATGATAAAGAATTTGTCGTCTTGACGGAACTGCTTATGATACAGCTGCTGAAACTCG

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 57

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 30

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCAGAAGGTTGAGCCTGTGATTATGGATGAGAGCGTGATGAAGGCATGTGAGGCTGTTGCTCGTGTTAGAGCTGAAGTTGATAGGCTGTCTGCTAAGgtgaaggaacattccatctccttccttatttgtttaagaatccatgtgtcatattatttcttgtgctcatgctgcttcctttgttttttttcctaaatgaatgttgtttcttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG