ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtcttttcagaaatctggtattcgtttcagttgtgatgatataggcaggcagctccagtaggtgttgttggataggcagaagaaattccccttctcagcaatctaaacctgtatgcttcttttcccttttgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGTTCTGCAATCAACTTCCGGAGGCA

Basic information

species	Zea mays
transcript	GRMZM2G142502_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G142502_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g39660.3 (Oryza sativa), 3'ss of exon 1

-------------------------------------------gtatgtcttttcagaaatctggtattcgtttcagttgtgatgatataggcaggcagctccagtaggtgttgt-tggatag---gcagaagaaattcccct--tctcagcaatctaaacctgtatgcttcttttcccttttgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGTTCTGCAATCAACTTCCGGAGGCA
                                              |  ||  |||  ||     |     |||   |||   |  | | |        ||     || |   || |  || |    |||  | |||| |       ||||||||    | |  || |      | |||| | |     |||||||||| || ||||| ||||| |||||||||||| | |||||| | ||||||||||||||  ||||                                 
gtatattcattcattcctctcccgaaatccccccctcctccctccctccctcctcaacaacaca-tccggatttggattggtttcttctcgatttcttcctttgacagattgcgtgtatattgctaacagtggcaatttcttcgggttcagCAATGCCCAACGTTAGGTCC---TCCCCTGTCG-----CAGATCTTCCTGGATGGCCATTGTTTTCGCCTCCTAAGCTTCAGTTGCAAAAGTGTACCAAGTGTCCCAG---------------------------------

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|78081830|gb|DV510242.1|DV510242

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAA---T--------G----                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|71438193|gb|DR819243.1|DR819243

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|149014312|gb|EE043889.2|EE043889

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|149079392|gb|EE168367.2|EE168367

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|148970848|gb|EE021623.2|EE021623

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|93284127|gb|EB676391.1|EB676391

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|148959588|gb|EC905543.2|EC905543

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|211357440|gb|FL362287.1|FL362287

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAAT                         ATCTTCCAGGGTGGCCGTTGTTCCCGCCTCCTAAGGTGCAGCTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

EST: gi|78082996|gb|DV511389.1|DV511389

EST:     TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATG---A----------T                         --CTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT
genomic: TGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 287

ATCATCACCACGTCCGGCCAAATCCAACCCCTCAAAATCCCGGACGCTGTTGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGAAATgtatgtcttt ... tgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGTTCTGCAATCAACTTCCGGAGGCA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 120

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attccccttctcagcaatctaaacctgtatgcttcttttcccttttgatctccagATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGTTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGTTCTGCAATCAACTTCCGGAGGCA