ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...ttcttctcataactaccttttgtatttctgttctgtatcttatgtaagtgccaatcattgcactcataggtctaaatttgttcaatatataaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC

Basic information

species	Zea mays
transcript	GRMZM2G467059_T03
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 3

ttcttctca--taactaccttttgtatttctgttctgtatcttatgtaagtgccaatcattgcactca-taggtctaaatttgttcaatatataaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC
|    || |  |   | |    | | ||     |   | |  |||||||       |  |   | | | || ||||||    | | || ||  || | ||||||||||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||| || || |||||||
taaagcttaatttgttgcaaaatatgttgacacttatttttctatgtaaacatgcgtattgaaagtgagtatgtctaa--cagcttaa-atggaattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATCCAGAGTGTCAAGGGGAAGGTGGTCATTGATGCATTTCGTCTCATTAATC

upper sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 3

---ttcttctcataactaccttttgtatttctgttctgtatcttatgtaagtgccaatcattgcactcataggtctaaatttgttcaatatataaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC
      |    |   |||| ||    | ||    | | |||   | |   |       ||    |    || ||||||  |  ||||| || | || |||||||||||||||||||| ||||||||||||||||| || |||||||| |||||||| ||||| |||||||| || || ||||||||||| ||||| ||||| |
acaaagtgtcaagtgctactttcccaagttaacgtttttataaaaag-gggcttagtgcaagttatatttacgtctaacatc-ttcaaaat-tgaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATCCAAAGTGTCAAGGGGAAAGTTGTCATTGATGCATTTCGCCTTATTAACC

upper sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 3'ss of exon 4

---------------------------------------------------------------ttcttctcataactaccttttgtatttct--gttctgtatcttatgtaagtgccaatcattgcactcataggtctaaatttgttcaatatataaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC
                                                                   |  ||| |         || || |   |||  |   |   | |      | |  ||  |   ||  | ||||||   ||    | | |  || ||||||||||||||||||||||||  || || ||||| || ||| | || || || || |||||||| || ||||| || |||||||| |||||  | || ||||
gtaagttaggcttgcactaactttcgttcttgcgttttgggtcccgaatgtgcaacggtggaaacaataccatgatctaacgcagtcttccatagttgggagaccggtatccccctccagaatcactgccagtgttctaaagcagtatcct-tgtgtatttgcagAGTTTTGAAGCTTTGAACCAAAGAGCGGTTGCGGTAGTGGTGGATCCAATTCAAAGTGTGAAAGGAAAGGTTGTGATTGATGCTTTCCGATTGATCAATC

upper sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 3

ttcttctcataactaccttttgtatttctgttctgtatctt-atgtaagtgccaatcattgcactc-ataggtctaaatttgttcaata--tataaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC
    ||| |    | | |||  | | | |  | | | |||| ||  || |||   |   |    |  |    | |    |     |||   | |  ||||||||||||||||||||||||| |  ||||| || || || ||  | || || ||||| |||||||| || ||||| || || ||||| || ||  | || || |
----tcttaaggtttcttttcttttcttttctatttctctttataaaaatgcttttaggtatgttttaccttttttctgtaacataattcttgtggatatgcagAGTTTTGAAGCTTTGAATCAAAGGGCGGTAGCAGTAGTAGTGGATCCAATCCAAAGTGTGAAAGGAAAGGTTGTGATCGATGCTTTTCGATTGATCAACC

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|211418133|gb|FL144508.1|FL144508

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|211410492|gb|FL144474.1|FL144474

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGAT
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGAT

EST: gi|94477725|gb|EB706683.1|EB706683

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|13389019|gb|BG462517.1|BG462517

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCC

EST: gi|211407935|gb|FL144457.1|FL144457

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|76282592|gb|DV022160.1|DV022160

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|148939805|gb|EC884507.2|EC884507

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|211415593|gb|FL144502.1|FL144502

EST:     ATCCTGGCTTCGGTTGCYGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGAT
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGAT

EST: gi|148966377|gb|EE017372.2|EE017372

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|149103923|gb|EE289338.2|EE289338

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|149026686|gb|EE046095.2|EE046095

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|17970155|gb|BM276920.1|BM276920

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|78091827|gb|DV520201.1|DV520201

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|211413037|gb|FL144482.1|FL144482

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATCCTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|78104620|gb|DV523038.1|DV523038

EST:     ATCCTGGCTTCGGCTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|148951536|gb|EC897265.2|EC897265

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|211405380|gb|FL144445.1|FL144445

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

EST: gi|211405377|gb|FL144442.1|FL144442

EST:     ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG                         AGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC
genomic: ATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATC

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: 45 (upstream exon), 49 (downstream exon)
Score: 315

GCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaa ... aaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 270

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 244

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aagtgccaatcattgcactcataggtctaaatttgttcaatatataaatatgcagAGTTTTGAAGCTTTGAACCCCAGGGCAGTTGCTGTTGTGATAGACCCCATCCAGAGTGTGAAGGGGAAGGTGGTTATTGATGCATTCCGCCTAATTAATC