ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagactatgaagctttaatgatccatttatatttatcttggaactttggaatcgcatgtatattgtttctatgagtctgtatctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC

Basic information

species	Zea mays
transcript	GRMZM2G026311_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G026311_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g36020.1 (Oryza sativa), 3'ss of exon 4

gtaagactatgaagcttta-atgatc-catttatatttatcttggaactttggaatcgcatgtatattgtttctatgagtctgtatctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC
             | |||| | |||  ||||   || |||    |  |  |  |||   || |    |  ||  |    ||  ||  || |||| |||||    |||| | || |||||||||||||||||||||||||||||||||||||||| || ||||||||||||||| |||||||| ||| | |||||||| |||| ||||||||||| ||
-------------gttttacaagattgcattcgaatctat----ggccaataaaattttatttgatgtacttggacagatcgttaattcttctggtcctttgcctgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTGCGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC

upper sequence: GRMZM2G026311_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g44790.1 (Oryza sativa), 3'ss of exon 2

gtaagactatgaagctttaatgatccatttatatttatcttggaactttggaatcgcat-gtatattgtttctatgagtctgt-atctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC
               | ||||  | |||| ||     | ||  ||  | | | ||| || |  || |  ||  |    ||||| |  || |||| ||||||  ||||| | || |||||||||||||||||||||||||||||||||||||||| || ||||||||| ||||| |||||||| ||| | |||||||| |||| ||||||||||| ||
---------------tataat--tgcattcatgccagttttacaagatcgcactcgaatcgattaattcttggacagatctgttaattcttctgatccttcgcttgtgaactctcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAAGAAAAAGCTTGTACGTTCTGTTCCTACAGAACTGAATAAAGATCACAATGGGATACTTGAGC

upper sequence: GRMZM2G026311_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G42650.1 (Glycine max), 3'ss of exon 3

gtaagactatgaagctttaatgatccatttatatttatcttggaactttggaatcgcatgtatattgtttctatgagtctgtatctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC
        ||     |||  | |||  | | | |  |     ||| ||||   |  ||||| |  |  ||  |    |  || | ||||   ||  |   |   |  |||  ||||| || ||||||||||||||||| ||||||||||| | || ||| ||||| ||||||||||| ||||| ||||| |||||||||| ||  || || |  |
--------attcc-ttttgttcatctttgtttctccactagagaaatttg---ttacatgtgtccttcttgaaccttttggtgtttcat--actgatctttaactaaattt-cagGTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACCGAGTTAAACAAAGACCACAATGAAATTCTAGAAC

upper sequence: GRMZM2G026311_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G11630.1 (Glycine max), 3'ss of exon 3

gtaagactatgaagctttaatgatccatttatatttatcttggaactttggaatcgcatgtatattgtttctatgagtctgtatctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC-
     | ||| |   |||  |  |   || || ||| |  |  |  |  | |||    |  || | ||   |    ||   || || || ||    |    |     | |  ||||| || ||||||||||||||||| ||||||||||| | || ||| ||||| ||||||||||| || || || || |||||||||| || ||| || |  | 
-----agtattacattttcct--tttgttcatctttgttctccacttgagaaatttgttacatgt-gtcctt----gttcata-ctgatgtgtaagt---gtaactaaatttcaggTGCTGGGTAGTGGTTTTGAAGTTATTTCTGTTGGAAAGAAAAAACTTGTTCGTTCAGTTCCAACTGAGTTGAACAAAGACCACAATGAGATTCTAGAACT

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|32828007|gb|CD967685.1|CD967685

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|71297620|gb|DR784761.1|DR784761

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|76021476|gb|DT948646.1|DT948646

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|78088647|gb|DV517040.1|DV517040

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|87155520|gb|DY400309.1|DY400309

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|78081791|gb|DV510203.1|DV510203

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|78088648|gb|DV517041.1|DV517041

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|148962831|gb|EE013751.2|EE013751

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|78087906|gb|DV516299.1|DV516299

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|32846677|gb|CD986358.1|CD986358

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|5018429|gb|AI714622.1|AI714622

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|101396301|gb|EB820076.1|EB820076

EST:     CATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: CATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|211125818|gb|FL435219.1|FL435219

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|32792491|gb|CD944727.1|CD944727

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         A
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcag-

EST: gi|32792491|gb|CD944727.1|CD944727

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         A
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcag-

EST: gi|71330916|gb|DR802256.1|DR802256

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|71330918|gb|DR802257.1|DR802257

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAA
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAA

EST: gi|76021477|gb|DT948647.1|DT948647

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|71297617|gb|DR784760.1|DR784760

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|76013036|gb|DT940206.1|DT940206

EST:     TGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAAGCA-GCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAA-GCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|93011965|gb|EB637485.1|EB637485

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|21809751|gb|BQ668069.1|BQ668069

EST:     TTGAATCATTATCTGAAGATGGCTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

EST: gi|78026633|gb|DV495020.1|DV495020

EST:     TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAA                         GTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG
genomic: TTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTG

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: 98

TGACTTACTAGATCTCCGCAAACTGCTCGGTCAGAAGAGGAAAGCTACTCTTGAATCATTATCTGAAGATGACTGTTTGCGTGCTATAAGCAAGCTAAAAgtaagactat ... ggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 97

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 67

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatattgtttctatgagtctgtatctcatctgctccttcctttgtggattcgcagGTCCTTGGTAGTGGTTTTGAAGTAATTTCTGTTGGGAGGAGAAAGCTTGTGCGTTCAGTTCCTACCGAATTAAATAAAGACCACAGTGGGATACTTGGGC