ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAGCGCCCCAACGCCGGCCTAGTCCTCAGCACCACCGCCCGCTTCTACGCCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctcttcaactgccatccctctagtctcagaagctatagcgtgttgctcttgctcctcaccctgtgtacccctgcaccgatgctag

Basic information

species	Zea mays
transcript	GRMZM2G019260_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G019260_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g14830.1 (Oryza sativa), 5'ss of exon 2

GGAGCGCCCCAACGCCGGCCTAGTCCTCAGCACCACCGCCCGCTTCTACGCCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctcttcaactgccatccct--ctagtctcagaagctatagcgtgttgctcttgctcctcaccctgt-gtacccctgcaccgatgctag
|||||| |||||||||||||| ||||||||||||| ||| |||||||||||| |||||||||| |||||||||   |||  |  |||| | ||||| ||||||||| |    |  | |   || |   | |   | |  ||    | || |  |   |||||||| || |||  |  | |||| ||| || ||||
GGAGCGGCCCAACGCCGGCCTCGTCCTCAGCACCAGCGCGCGCTTCTACGCCATCGTCCGCCCGCTCCGCGACGAGCTCAGCCACGACTCCTGGGCATGGgtgagccccgagccccagatttctcgaacaaactttactagtagcatcgcggagaa-ttgctccttactctgccgagcacctgtacc-atactag

upper sequence: GRMZM2G019260_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g48160.1 (Oryza sativa), 5'ss of exon 3

GGAGCGCCCCAACGCCGGCCTAGTCCTCAGCACCACCGCCCGCTTCTACGCCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACG---CTTGGGCCTGGgtgagcgctc-----ttcaactgccatccctctagtctcagaagctat-agcgt--gttgctcttgctcctcaccctgtgtacc-cctgcaccg-atgctag-----------
   |||||||||||||||||| ||||||| ||||||||| ||||||||||||||||||| ||| | |||||||   ||| ||  |||||   | ||||| ||||||||| | |       ||  |    || | |     | || ||| || | | |  |       |  |||| || ||||||    ||||  ||  ||| ||            
---GCGCCCCAACGCCGGCCTCGTCCTCATCACCACCGCTCGCTTCTACGCCGTCGTCCTCCCGCCCCGCGACCAGCTCACCCACGACGAATCCTGGGCATGGgtgagcccccgaaaccccagattatttctcacacaatttagtagccatcaccatcagggagaactaatccttactctgtgtggtacctgtcccatatggtaaattgctactag

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|211063636|gb|FL185551.1|FL185551

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|78089475|gb|DV517849.1|DV517849

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|78093392|gb|DV521766.1|DV521766

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|101392374|gb|EB818116.1|EB818116

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|76285163|gb|DV024731.1|DV024731

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|211060651|gb|FL185544.1|FL185544

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAGAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|211063635|gb|FL185550.1|FL185550

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|211060654|gb|FL185547.1|FL185547

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|74234775|gb|DT642689.1|DT642689

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|211060650|gb|FL185543.1|FL185543

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|71447563|gb|DR828613.1|DR828613

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|148978577|gb|EE026218.2|EE026218

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|211060652|gb|FL185545.1|FL185545

EST:     CCGTCGTCCGCCCCCTCCGCGACASSCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|91867695|gb|EB399758.1|EB399758

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|76017987|gb|DT945157.1|DT945157

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|101390541|gb|EB817205.1|EB817205

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCCTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

EST: gi|71308540|gb|DR790509.1|DR790509

EST:     CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGG                         GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA
genomic: CCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACA

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: 46 (upstream exon), 48 (downstream exon)
Score: 115

GGAGCGCCCCAACGCCGGCCTAGTCCTCAGCACCACCGCCCGCTTCTACGCCGTCGTCCGCCCCCTCCGCGACAGCCTCCCCGCCGACGCTTGGGCCTGGgtgagcgctc ... ccgatgctagGCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129