ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagattctatcagaggtccagaacattatagccttagagggttgactttatttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA

Basic information

species	Zea mays
transcript	GRMZM5G840955_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9

--gtaagat-tctatcagaggtccagaacattatagccttagagggttgacttta-tttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
    | ||| | |  ||    |||       |  |     | |   || |||| | |||   ||||  || ||   ||||| ||||||||||| || |||||||| |||||||| |||||||| ||||||||||||||||||||||| ||||| ||||| || ||||| ||||||||||
gtaaaggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactc-cagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA

upper sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9

-------------------------------------------gtaagattctatcagaggtccagaacat-------tatagccttagagggttgactttatttccatttcatatgacc-tacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                                            |||  | || | |    ||   ||  |        |||    ||      |   |  ||||   |||  ||      ||||||||||||||| ||| || |||||||| || ||||| |||||||| || |||||||||||||| || ||||| || || || ||||| |||||||| || |
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA

upper sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G07280.1 (Glycine max), 3'ss of exon 8

----------------------------------------------------gtaagattctatcaga---ggtccagaacattatagccttagagggttgactttatttccatttcatatgacc-tacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                                                     | |  | || | | |   | |   | | ||||       |   | |  | ||| |||   |||  ||      |||||||||||||||  || || |||||||| || |||||||||||||| || ||||| |||||||| || ||||| || || || ||||| |||||||| || |
gtaatttcccaagttacagttgtatgcatgacatttttcctttttaatttcctttaactgctcttaaatctgtttttgcatattactaagccactcgttacattttttttttgttttttaacttagtacagGTTGATGAGAAAGGTATGCGCTGGTTTTATACTGGTGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA

upper sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 9

---------------------------------------------------------------------------------------------------------------gta-agattctatcagaggtccagaacattatagccttagagggttgactttatttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                                                                                                                || | | | | | | ||      |||| |  | | |  ||       | ||  |  ||| || | ||  ||||||||||||||||||||||| |||||||| || |||||||| ||||| ||||| || ||| |||| |||||||| || ||||||||||| || ||||| || |
gtaataagtaacttcttttgtggataggtgcctgtattggcatttgtatttactttttgtgtatttatatatatatatatgtgtgtgtatgtatatatacatacacaatacatatatactttcttatag---tgcaacacttcaacttgtgaatagctgcgttggtgacatatcgtctg--ctacagGTTGATGAGAGGGGCATGCGCTGGTTTTATACTGGTGACATTGGACAGTTTCAACCTAATGGTTGCCTTGAAATAATTGACAGGAAGAAGGATATTGTTA

upper sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ26722 (Selaginella moellendorffii), 3'ss of exon 8

gtaagattctatcagaggtccagaacatta-tagccttagagggttgac-tttatttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                 || ||     | | |  ||||  || ||| |  |||| |||  |||  | |||     ||||||| |||||||||||  | ||||||||||||||||| ||||| || |||||||| ||||| ||| | || ||| | ||| |||| || || || || |
-----------------gtacaacttttcagtttccttgaagcgttcatgtttaattcgtttttttgtga-----agGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTA

upper sequence: GRMZM5G840955_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8

gtaagattctatcagaggtccagaacatta-tagccttagagggttga--ctttatttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                 || ||     | | |  ||||  || ||| |  ||| |||    |||  | |||     ||||||| |||||||||||  | ||||||||||||||||| ||||| ||||||||||| ||||| ||||| || ||| | ||| |||| || || || || |
-----------------gtacaacttttcagtttccttgaagcgttcatgcttaattgggtttttttgtga-----agGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA

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|67018930|gb|CO447679.1|CO447679

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|22715395|gb|BU197739.1|BU197739

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|211013565|gb|FL361178.1|FL361178

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|60358827|gb|DN225800.1|DN225800

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|211306727|gb|FL367401.1|FL367401

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|5761807|gb|AI966960.1|AI966960

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|87156299|gb|DY401088.1|DY401088

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|26559525|gb|CA831760.1|CA831760

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|211176149|gb|FL381702.1|FL381702

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|40335028|gb|CK369098.1|CK369098

EST:     CAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: CAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|21809634|gb|BQ667952.1|BQ667952

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

EST: gi|56382586|gb|CV985255.1|CV985255

EST:     TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAG                         GTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC
genomic: TAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTC

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), 49 (downstream exon)
Score: 395

TTCTGATTCTCCAATGCCGAGAGGAGAGGTCGCGGTTGGTGGACACAGTATAACAAAAGGTTATTTCAACAATGAAGCAAAGACGAACGAAGTATACAAGgtaagattct ... tgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 541

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 460

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 622

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cagaacattatagccttagagggttgactttatttccatttcatatgacctacagGTTGATGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGTCAGTTCCATCCTGATGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA