ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...ctcacaagttcttcctgctcaccagtccacttgaatccaaattttagttttggtgatctacatcttgctgcatacatgacatttggaactcttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGCAAATGGTCACTTCTTCAGAACAGGGTAACCACCTCTCCAGGCCATCATG

Basic information

species	Zea mays
transcript	GRMZM2G085602_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G085602_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g56820.2 (Oryza sativa), 3'ss of exon 6

ctcacaagttcttcctgctcaccagtccacttgaatccaaattttagttttggtgatct---acatcttgctgcatacatgacatttggaactcttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGCAAATGGTCACTTCTTCAGAACAGGGTAACCACCTCTCCAGGCCATCATG------------------------------
                             ||| ||     |||| | | ||||||  ||   ||||| || ||||||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||  ||||||    ||| |  ||   || |      |||   |||||| ||   |||                              
-----------------------------cttaaacttctatttaactattggtgtgctttaacatcatgatgcatacatgacatttc-aactcttggagcaggattcttacccgccattttctttgaagGCCTTTCTGAACAAGTAAG-GTGCAACCAATCAATCGTTAGAAAGATCACCTCCAGGGCTCCAGTCC--TATGGCCACCAGAGTTCCCTTCAGAATGTGTAAA

upper sequence: GRMZM2G085602_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g56820.1 (Oryza sativa), 3'ss of exon 6

ctcacaagttcttcctgctcaccagtccacttgaatccaaattttagttttggtgatct---acatcttgctgcatacatgacatttggaactcttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGCAAATGGTCACTTCTTCAGAACAGGGTAACCACCTCTCCAGGCCATCATG---
  || ||        | ||   |||||||||| ||     |||| | | ||||||  ||   ||||| || ||||||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||  ||||||    ||| |  ||   || |      |||   |||||| ||   |||   
tccataatcataagttacta--cagtccacttaaacttctatttaactattggtgtgctttaacatcatgatgcatacatgacatttc-aactcttggagcagGATTCTTACCCGCCATTTTCTTTGAAGGCCTTTCTGAACAAGTAAG-GTGCAACCAATCAATCGTTAGAAAGATCACCTCCAGGGCTCCAGTCC--TATGGCC

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|71429535|gb|DR810585.1|DR810585

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC

EST: gi|32829902|gb|CD969580.1|CD969580

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC

EST: gi|113844161|gb|DW954258.1|DW954258

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTC

EST: gi|45567661|gb|CK985682.1|CK985682

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC

EST: gi|71429534|gb|DR810584.1|DR810584

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC

EST: gi|33097708|gb|CF057668.1|CF057668

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC

EST: gi|211404105|gb|FL439001.1|FL439001

EST:     TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAG                         GATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC
genomic: TCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGC

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), 47 (downstream exon)
Score: 60

CACATGCTAATCTTCCAGCATATTCATCGTTGGAGAGGGTGGTCCAGCAAGCGACTGTGGTTAGACAATACCTACAGCAGGAAGTTGGCAAGgtaaatatcg ... cttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGCAAATGGTCACTTCTTCAGAACAGGGTAACCACCTCTCCAGGCCATCATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agttttggtgatctacatcttgctgcatacatgacatttggaactcttggagcagGATTCTTACCCACCATTTTCTTTGAAGGCCTTTCTGAGCAAGTAAATGTGCAAATGGTCACTTCTTCAGAACAGGGTAACCACCTCTCCAGGCCATCATG