ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGCGGAGAGCTACCCTGCCTACCCAGATTTCGCGGCCATTCCCCTTTTCGTCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagtttttcccgctcatttttacaacatttctcgtttgctgtacgtatcattatcaacgatgctcgagccagttattttatagagtacgaagagag...

Basic information

species	Zea mays
transcript	GRMZM2G315726_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G315726_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g49590.1 (Oryza sativa), 5'ss of exon 1

GGCGGAGAGCTACCCTGCCTACCCAGATTTCGCGGCCATTCCCCTTTTCGTCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgta---gtttttcccgctcatttttacaacatttctcgtttgctgtacgtatcattatcaacgatgctcgagccagttattttatagagtacgaagagag
||||||||||||||| |||||| | || |||||||| || ||| | |||| ||||||| || ||| ||||||||   |||||||||||||||| |||||||||||    |||||  | | || ||||  | ||    | | ||| | |||  | | | |   |  | ||     |  ||     |    |  |     || | 
GGCGGAGAGCTACCCGGCCTACTCGGACTTCGCGGCGATCCCCTTATTCGCCGTCTTCCTCTTCGCCGTCCGTTATCTCCTCGACCGCTTCGTCTTCGAGgttgtgatggttttcacggttctttttccccaccacgcccattttc-gtat-tgttactgg-agtggtgagatggagagaggggtggggggcttttctgacaa

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|58029540|gb|CX724967.1|CX724967

EST:     TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAG                         TGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC
genomic: TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagttt ... ttgttcatagTGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC

EST: gi|211275405|gb|FL063658.1|FL063658

EST:     TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAG                         TGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC
genomic: TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagttt ... ttgttcatagTGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC

EST: gi|78084141|gb|DV512534.1|DV512534

EST:     TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAG                         TGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC
genomic: TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagttt ... ttgttcatagTGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC

EST: gi|58029485|gb|CX724912.1|CX724912

EST:     TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAG                         TGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC
genomic: TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagttt ... ttgttcatagTGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC

EST: gi|47962327|gb|CN845036.1|CN845036

EST:     TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAG                         TGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC
genomic: TCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagttt ... ttgttcatagTGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGC

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 3 RNA-Seq libraries.

Block sizes: 17 (upstream exon), 49 (downstream exon)
Score: 5

GGCGGAGAGCTACCCTGCCTACCCAGATTTCGCGGCCATTCCCCTTTTCGTCGTCTTCTTCCTCGTCGTCCGTTTCTTCCTCGACCGCTTCGTATTCGAGgttgtagttt ... ttgttcatagTGGTTAGCCAGGAAGCTGATTTTCAAGGAGGAGGATGAGAAGAAGCTTGGCCCTACTACATATGCAGGCAAGAGAAAGATCAGGAAATTTAAAGAATCAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 221