ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaagaatgcctttgctgtttaattctgctctagaaattttctttaccgttcactaagtcgtatggttttttgtatgatgtcttccttttgtgggcggccttatttggtaacaaggttttaaaatgcccacagcttaagcaagtagatactaactatggagtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGAGGGGACTGTGATCATCAGGGACAACGTAGAGGTGTTGGTGAAGGTACAA

Basic information

species	Zea mays
transcript	GRMZM2G164916_T02
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G164916_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g01450.1 (Oryza sativa), 3'ss of exon 5

gtaaagaatgcctttgctgtttaattctgctctagaaattttctttaccgttcactaagtcgtatggttttttgtatgatgtcttccttttgtgggcggccttatttggtaacaaggttttaaaatgcccacagcttaagcaagtagatactaactatggagtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGAGGGGACTGTGATCATCAGGGACAACGTAGAGGTGTTGGTGAAGGTACAA
                                                                    | || |  |  ||  |   | |        |  |   |||  ||| |  | || ||     || ||   ||  ||  |  || |    |   |  |||  |||||||||| |||| ||||| || |||||||||||||| |||||||||||||| ||||| |||||  |||||||||  || |||||||| |||||| |||||
--------------------------------------------------------------------tgttagcgtt-tgagtcattataagaaaatgattcccttgacaactaa-tgttgaacaattca-agtaaaaataataatctaatgttgaacaatgggtttcagGTGTGACGTAACATACATTCTCCTGGAGATGGACCGGATTCTAAGGCCTGAAGGGACAGTGATTTTCAGGGACACGGTGGAGGTGTTAGTGAAGATACAA

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|26456628|gb|CA828211.1|CA828211

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|22472582|gb|BU037062.1|BU037062

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|76018660|gb|DT945830.1|DT945830

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|20507065|gb|BQ279469.1|BQ279469

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGCTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|67018896|gb|CO447645.1|CO447645

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|87156846|gb|DY401635.1|DY401635

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|26558531|gb|CA830766.1|CA830766

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|83278806|gb|DV942814.1|DV942814

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

EST: gi|71775256|gb|DR973134.1|DR973134

EST:     ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAG                         GTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTTTAAGGCCTGA
genomic: ACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGA

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), 45 (downstream exon)
Score: 45

TTATTGGCACGTACCATGATTGGTGTGAGGCTTTCTCAACGTACCCGAGGACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatg ... gtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGAGGGGACTGTGATCATCAGGGACAACGTAGAGGTGTTGGTGAAGGTACAA

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 29

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 27

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gttttaaaatgcccacagcttaagcaagtagatactaactatggagtggtcgcagGTGTGACATAACGTACATCCTACTGGAGATGGACCGAATTCTAAGGCCTGAGGGGACTGTGATCATCAGGGACAACGTAGAGGTGTTGGTGAAGGTACAA