ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaatcattcagttgcactgtacgctctttatttctagtttctaaactagaactgacttacaacacaacagagttcagaagattgtgttttgaaa...

Basic information

species	Zea mays
transcript	GRMZM2G097277_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G097277_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 5'ss of exon 12

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaatcattcagttgcactgtacgctctttatttctagtttctaaactagaactgacttacaacacaacagagttcagaagattgtgttttgaaa----
|| |||||||| ||||||||||| ||||| || ||| |||||||||| ||||| |||||||||||||| ||||||||||| ||||||||||| || ||||||  | |  || |||||||||||      ||   ||  |  |       || |     |       ||  || || | | | | |  |  ||||   ||     
ACATGGGGTTCAGTTCGTGCAGCGATGGGTCATCCACAACCCTTTAACCTTGACTATGTTTCAATAGGGAATCAAGAATGCTGGATGCTCTATTACAGAGgtctgtagctc-ttcagttgcac---gtccttcctaacttcataccaagaattgatgtttgaacttaatgcatcatattcctgtacttcatgttggaaattttt

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|67024258|gb|CO453007.1|CO453007

EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

EST: gi|211168064|gb|FL062250.1|FL062250

EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

EST: gi|67026679|gb|CO455428.1|CO455428

EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

EST: gi|71757747|gb|DR955684.1|DR955684

EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

EST: gi|5895641|gb|AW036887.1|AW036887

EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

EST: gi|67042721|gb|CO468976.1|CO468976

EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

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: 101

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 128

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59