ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagtactgtgtgtctgactgtctgttatgggttccactacatttcgggagggggaggggagcagagcagctgtcgaccgcgtcccgacgtcgcttttgctggatcgaatgaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G141922_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G141922_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g02130.1 (Oryza sativa), 5'ss of exon 6

GCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagtactgtgtgtctgactgtctgttatgggttccac-tacatttcgggagggggaggggagc-----agagcagctgtcgaccgcgtcccgacgtcgcttttgctggatcgaatgaatgcag
| ||||||||||| ||| |||| ||||| ||||||||| |||| |||||| |||| ||||| |||||||| || ||||| ||||| ||||| || || ||||||| | ||   | | ||   || || ||| | |  |   |  | ||    | |      |  | ||     ||   || |||       || | |  ||                           
GAAGCACGTCGCTTCATTTGGCTGCTCGTAGCGGGAACTTGGATTGCATCAGGAAGCTGCTTGCCTGGGGAGCTGATCGGCTCCAAAGGGATTCGGCTGGgtgagaactag-atctttccccct-tcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagtgaagttcaggtgtt--------------------------

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|89756253|gb|DY686344.1|DY686344

EST:     CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|87153855|gb|DY398644.1|DY398644

EST:     CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAAG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGGGGCGTGCGCGGC
genomic: CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|94480421|gb|EB709379.1|EB709379

EST:     CTCCAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|71762078|gb|DR960015.1|DR960015

EST:     GGCGCGGATCGTCTCCAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: GGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|71435966|gb|DR817016.1|DR817016

EST:     CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|76284382|gb|DV023950.1|DV023950

EST:     CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|91869237|gb|EB400304.1|EB400304

EST:     CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|101396548|gb|EB820200.1|EB820200

EST:     CAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|74241429|gb|DT649343.1|DT649343

EST:     CAGAGGGACTCAGCAGG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC
genomic: CAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

EST: gi|19057993|gb|BM736660.1|BM736660

EST:     CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAAG                         GAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGGGGCGTGCGCGGC
genomic: CGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGC

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: 127

GCAGCACGTCGCTGCATCTGGCCGCTCGAAGCGGGAACCTGGACTGCATCCGGAAACTGCTCGCCTGGGGCGCGGATCGTCTCCAGAGGGACTCAGCAGGgtgagtagta ... atgaatgcagGAGGATTCCTTACGCCGTGGCGCTGAAGCGCAACCACGCGGCGTGCGCGGCGCTGCTGAACCCGTCGGCGGCGGAGCCCATGGTGTGGCCTTCCCCGCTC

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 44

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69