ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtgagtcgatcgatttttctttctttctttcccgcctcttcaagtccgtgtgatgtggtctgaattcctctgttggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAG

Basic information

species	Zea mays
transcript	GRMZM2G095141_T03
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G095141_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 6

gtaagtgagtcg-atcgatttttctttctttctttcccgcctcttcaagtccgt-----gtgatgtggtctga--attcctctg--ttggtc-tctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAG
    || ||||  ||    ||     ||| ||   || |    || ||           |  || || |||||  |||    |   ||| || ||  ||||| || ||||||||| ||| |||||| |||| |||| |||   ||||  | ||||| || ||||||||||||||||| |||  |||||| |||||||||
----gtaagtcacataagcttgatgatctatcgagcctgaaagttaaaaagaacagacagcaatctgatctgagaatttgcataatttgatcgtcatagGTATGTTTCATGTGTGGTTGGTTGCCCTGTTGAAGGCACAATTCATCCATCAAAGGTAGCATACGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAG

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|76016005|gb|DT943175.1|DT943175

EST:     TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGC
genomic: TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGC

EST: gi|71318555|gb|DR796038.1|DR796038

EST:     TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGC
genomic: TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGC

EST: gi|148950048|gb|EC895580.2|EC895580

EST:     TCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGC-TGCCCCCGTTGGAGGCGCAACCGATCCGG
genomic: TCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTG-CCCCGTTGGAGGCGCAACCGATCCGG

EST: gi|211081279|gb|FL464186.1|FL464186

EST:     TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAAACCGATCCGG
genomic: TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGC-AACCGATCCGG

EST: gi|91872713|gb|EB402670.1|EB402670

EST:     TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGCTTGCCCCNGT-GGAGGCGCAACCGATCCGG
genomic: TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCC-GTTGGAGGCGCAACCGATCCGG

EST: gi|211139185|gb|FL464627.1|FL464627

EST:     TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGC
genomic: TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGC

EST: gi|148951196|gb|EC896884.2|EC896884

EST:     TACCGCGGCGTCACAGCGGCTGCCNAGAAACACGGGCTAAGCATCCGGGG                         GTACGTGTCATGTGTGATTGCTTGCCCCG
genomic: TACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCG

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: 46 (upstream exon), 49 (downstream exon)
Score: 34

CCTTCTCCAGGTCCAACATCAACTGCACCATCGAGGAGAGCCTTGCTCGGTACCGCGGCGTCACAGCGGCTGCCAAGAAACACGGGCTAAGCATCCGGGGgtaagtgagt ... ggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcccgcctcttcaagtccgtgtgatgtggtctgaattcctctgttggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAG

                                               tctctc  CT-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgagtcgatcgatttttctttctttctttcccgcctcttcaagtccgtgtgatgtggtctgaattcctctgttggtctctcagGTACGTGTCATGTGTGATTGCTTGCCCCGTTGGAGGCGCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT