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

gtagactatacctatacgtgcatgcgcatccacccataatccgtgcatgcatgcatgattattgacactaatgtccttattactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCCCGGCGAGCGACGTGGTGCAGCTGTACCAGTCCAACGGCATCAACCTGAT

Basic information

species	Zea mays
transcript	GRMZM2G065585_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G065585_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g71340.1 (Oryza sativa), 3'ss of exon 1

--------gtagactatacctatacgtgcatgcgcatcc---acccataatccgtgcatgcatgcatgattattgacactaatgtccttattactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCCCGGCGAGCGACGTGGTGCAGCTGTACCAGTCCAACGGCATCAACCTGAT
        | | |  | |  |||| |            |   |   || |    | ||  |    |  |  |  ||  ||||| |    | |   | ||||  || ||||| |||||||||||||||||||||| |||  ||||||||||  || |||||||||| |||||||| ||| |||||||||||||| ||   ||
ttgaatttggaaaaaaaagttataagatggaatattctctaaagggattaataatccactcccaaacaaaaag-gagtctaatatatcaaatcaaacacagTGGTGCAATCTATCGGCGTGTGCTACGGCGTGATCGGGAACAACCTGCCGTCGCCGAGCGACGTCGTGCAGCTCTACAAGTCCAACGGCATCGACTCCAT

upper sequence: GRMZM2G065585_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g71400.1 (Oryza sativa), 3'ss of exon 1

-----------------------------------------------------------------------------gtagacta-tacctatacgtgcatgcgcatccacccataatccgtgcatgcatgcatgattattgacactaatgtccttattactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCCCGGCGAGCGACGTGGTGCAGCTGTACCAGTCCAACGGCATCAACCTGAT
                                                                              || |    |  | || |||  ||  | |        |||    |    |   |  | |   |  | | |  |     || || | |||||  || |||||||| |||||||||||||||||||||||| ||||||||||  || |||||||||| ||| |||| |||||||| || || ||| ||   ||
gtaagtatatatatcacgtgtattagggcctacaccctccattcccaataagaagcaactttcatggatgaatttggataaatagctgtccattcgtttata-gaagttgtttttaagagttaggagtgcgtgtaac-gtatatattgttcgttctactaatcaacagTGGTGCAATCCATTGGCGTGTGCTACGGCGTGAACGGCAACAACCTGCCGTCGCCGAGCGACGTCGTGAAGCTCTACCAGTCGAAGGGGATCGACTCCAT

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|211203532|gb|FL012155.1|FL012155

EST:     CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAG                         GAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCC
genomic: CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAGgtagactata ... tactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCC

EST: gi|8367548|gb|BE050493.1|BE050493

EST:     CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAG                         GAGTCCAATCCATCGGCGTGTGCCTACGGCGTGAACGGCGACAACCTGCCC
genomic: CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAGgtagactata ... tactaaacagGAGTCCAATCCATCGGCGTGTGC-TACGGCGTGAACGGCGACAACCTGCCC

EST: gi|149206611|gb|ES702207.1|ES702207

EST:     CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAG                         GAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCC
genomic: CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAGgtagactata ... tactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCC

EST: gi|211203531|gb|FL012154.1|FL012154

EST:     CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAG                         GAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCC
genomic: CATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAGgtagactata ... tactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCC

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 3 RNA-Seq libraries.

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1111

CTGACCACCGCCGATCCTTCCAAGATGGCGAGGCAGGGTGTCGTCGCTTCCATGCATGCGCTGGCATTGCTTCTCGGAGCATTCGCAGCCATTCCTACAGgtagactata ... tactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCCCGGCGAGCGACGTGGTGCAGCTGTACCAGTCCAACGGCATCAACCTGAT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 323

Block sizes: 32 (upstream exon), 39 (downstream exon)
Score: 7

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ataatccgtgcatgcatgcatgattattgacactaatgtccttattactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCCCGGCGAGCGACGTGGTGCAGCTGTACCAGTCCAACGGCATCAACCTGAT

                              cactaat  putative branch site (score: 7)
                                      tccttatt  CT-rich tract
                                         ttattactaaa  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagactatacctatacgtgcatgcgcatccacccataatccgtgcatgcatgcatgattattgacactaatgtccttattactaaacagGAGTCCAATCCATCGGCGTGTGCTACGGCGTGAACGGCGACAACCTGCCCCCGGCGAGCGACGTGGTGCAGCTGTACCAGTCCAACGGCATCAACCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG