ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttcttaatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagttgttgtgtgattcttgtgccaattgaact...

Basic information

species	Zea mays
transcript	GRMZM2G002440_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G002440_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g25090.2 (Oryza sativa), 5'ss of exon 5

TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttct--taatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagtt-gttgtgtgattcttgtgccaattgaact
||||||  | |||||||| ||||||||||||| |||   |||  ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  |||   ||||  |  | |  | ||  || |   | |   | | ||    ||  |  | | |||||  | |   | |      ||    |||    
TGATCCACTTAATGAGAAATTTGATCCAAATAAGCATGCTGCGCTTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctcttccgataattttggtatagggtttttacccc-ctttctcttctgaaataagagctcattcaagtccggtacttaacctcaatgtttgttggt--

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|5922290|gb|AW055579.1|AW055579

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|5739690|gb|AI947266.1|AI947266

EST:     ATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: ATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|50332490|gb|CO527616.1|CO527616

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|5819185|gb|AI987391.1|AI987391

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|13237180|gb|BG355194.1|BG355194

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|37394200|gb|CF634371.1|CF634371

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|67042408|gb|CO468663.1|CO468663

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|18659614|gb|BM500430.1|BM500430

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|32934212|gb|CF039024.1|CF039024

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|5607682|gb|AI901349.1|AI901349

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|88754856|gb|DY538997.1|DY538997

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGGTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|21828625|gb|BQ703309.1|BQ703309

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|74234069|gb|DT641983.1|DT641983

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

EST: gi|16378404|gb|BI992428.1|BI992428

EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAG                         GTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTC

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: 222

TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcattt ... tttttttcagGTTGGCTACATGTTACATGATCGTGTTCTTCGCCCCGCTGAAGTTGGTGTCACTGAAGGTGGTCCAACTGAAGAAGAGCCAGAGGAGTAATCTAGATCAA

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 231

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 297

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttcttaatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagttgttgtgtgattcttgtgccaattgaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT