ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAAGGTGACTACTACCGTTACTTGGCTGAATTTAGCACTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaacttccaaatgttgtacgtaggctcaaatgagccttttggtaaagcctatcccttcctgttaaaatgacaaacatttgctgcag

Basic information

species	Zea mays
transcript	GRMZM2G145213_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g39540.1 (Oryza sativa), 5'ss of exon 3

GAAAGGTGACTACTACCGTTACTTGGCTGAATTTAGCACTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaacttccaaatgttgtacgtaggctcaaatgagccttttg-gtaaagcctatcccttcctgttaaaatgacaaacatttgctgcag-----------------------------------------------------
||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||  |||||||||| ||||||||||||||||||  ||| |||  |||| | ||||  | |||||||||| | | | |  | || |||     | |   ||   |  || ||||| || |||                                                       
GAAGGGTGACTACTACCGTTACTTGGCTGAATTTAGCACTGGAACTGAAAAGAAGGCTGCTACTGATCAGTCCCTTATGGCCTATCAGgtgtgaaatcttttaaatatagtacacatgctcaaatgaacttctggtattaatccttggtttccacctttggaaaactaacatatgttgctccagcacgccatggttgttgcctccagtgagctttctcctgcccatcaattcag

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|78109295|gb|DV527711.1|DV527711

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|6431859|gb|AW172063.1|AW172063

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|22935751|gb|BU572026.1|BU572026

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|74234408|gb|DT642322.1|DT642322

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|211267022|gb|FK966686.1|FK966686

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|74240176|gb|DT648090.1|DT648090

EST:     TGGAATCTGAAA-GAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCCTGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCCAATCCGG
genomic: TGGAA-CTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|6227145|gb|AW155674.1|AW155674

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|211267020|gb|FK966684.1|FK966684

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCTTGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|71302156|gb|DR787186.1|DR787186

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACTAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|5566988|gb|AI881899.1|AI881899

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|31353761|gb|CD438118.1|CD438118

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|78093195|gb|DV521569.1|DV521569

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|67020921|gb|CO449670.1|CO449670

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|101382257|gb|EB813184.1|EB813184

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|44681886|gb|CK786934.1|CK786934

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|71448133|gb|DR829183.1|DR829183

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

EST: gi|71444597|gb|DR825647.1|DR825647

EST:     CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAG                         CATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG
genomic: CTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGG

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), 48 (downstream exon)
Score: 160

GAAAGGTGACTACTACCGTTACTTGGCTGAATTTAGCACTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaac ... tttgctgcagCATGCCATGGTTGTCGCCTCCAGTGAGCTCTCACCTGCTCACCAAATCCGGCTTGGCCTTGCCCTCAATTTGTCGGTCTTCTTTTATGAGATAATGAACT

Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 52

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 101

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGGTGACTACTACCGTTACTTGGCTGAATTTAGCACTGGAACTGAAAAGAAAGCTGCCTCTGATCAGTCACTTATGGCCTATCAGgtgctaaaacttccaaatgttgtacgtaggctcaaatgagccttttggtaaagcctatcccttcctgttaaaatgacaaacatttgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC