ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtattgccatgtgggtagcacttctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG

Basic information

species	Zea mays
transcript	GRMZM2G029559_T02
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 6

gtatgtattgccatgtgggtagcact---tctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG
||| |||| | || ||||||| |  |   |  | ||   ||||    ||||  ||| || || |  | |||  ||||||  || ||| |||| |||||||||||||||||| |||| ||| |||| ||||| || |||||||||||||||| ||||||||| ||||||||||| ||||
gtaagtatggtcaagtgggtatcgttgtgttctccttgttagca-atttgtgatctaatcttgtt-tctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG

upper sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 5

gtatgtattgccatgtgggtagcacttctttctcaatagcttga----ttgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG
||| |||| | || ||||||  ||     || ||  |   |       |||| |||| || || |  | ||| |||||||  || ||| |||| |||||||||||||||||| |||| ||| |||| ||||| || |||||||||||||||| ||||||||| ||||| ||||| ||||
gtaagtatggtcaagtgggtgtcatagtgttttccttgtgtcagcaatttgttgtctaatcttatt-tctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG

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|17921484|gb|BM259135.1|BM259135

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCG
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCG

EST: gi|15426721|gb|BI542543.1|BI542543

EST:     TTGGAAAGGGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGGG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|32823439|gb|CD963161.1|CD963161

EST:     TGGAAAGTGGTTGGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TGGAAAGTGGTT-GTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|17921811|gb|BM259462.1|BM259462

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCG
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCG

EST: gi|56382464|gb|CV985133.1|CV985133

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|21987889|gb|BQ779417.1|BQ779417

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|32942861|gb|CF047680.1|CF047680

EST:     TGGAAAGTGGTTGGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TGGAAAGTGGTTG-TACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|32807718|gb|CD959952.1|CD959952

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|30087596|gb|CB885802.1|CB885802

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCA
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCA

EST: gi|32908341|gb|CF013154.1|CF013154

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|213175370|gb|FM190159.1|FM190159

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|26456546|gb|CA828129.1|CA828129

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|211045445|gb|FL056738.1|FL056738

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCC-TATGCTGCTGTG                         ACAGAAGAATC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATC

EST: gi|20301474|gb|BQ164417.1|BQ164417

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|31406016|gb|CD484748.1|CD484748

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGNTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|74237946|gb|DT645860.1|DT645860

EST:     TTGGAAAGTGGTTGTACCCACGTATGGNGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|31359821|gb|CD444178.1|CD444178

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|21331579|gb|BQ486960.1|BQ486960

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

EST: gi|548017|gb|T25217.1|T25217

EST:     TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTG                         ACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC
genomic: TTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAAC

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: 507

CCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTGTGgtatgtattg ... tgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 219

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 346

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agcacttctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG