ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGATGACATGATTGCTGTAAATAATATGCGTTGCTTATGTGGGCCTGATACCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattgtaggttatttcttggcttctatttctatatttaatctggatctgaagatgtattcttttcttcctgttgataacag

Basic information

species	Zea mays
transcript	GRMZM2G052880_T01
intron #	16
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G052880_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 5'ss of exon 12

TGATGACATGATTGCTGTAAATAATATGCGTTGCTTATGTGGGCCTGATACCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattgtag-gttatttcttggcttctatttctatattta---------atctggatctgaagatgtattcttttcttcctgttgataacag
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TGATGACATGATTGCTGTGAGTAATATGCGTTGCTTATGTGGCCCTGACACCAAAAAGTCCTCGGGAGGAGGTTTTACGTTTAAATTTGATGTTCACAAGgtaaacgaaatattgctttctttttggttctttctgaacatttatctgctaccaacctgatctcatgatgtattaattgattcctactgataacag

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|67022604|gb|CO451353.1|CO451353

EST:     CCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAG                         AAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA
genomic: CCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattg ... ttgataacagAAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA

EST: gi|76911270|gb|DV164216.1|DV164216

EST:     CCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAG                         AAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA
genomic: CCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattg ... ttgataacagAAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA

EST: gi|6827451|gb|AW331094.1|AW331094

EST:     ATTTGATGTTCACAAG                         AAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA
genomic: ATTTGATGTTCACAAGgtaaacattg ... ttgataacagAAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA

EST: gi|76908403|gb|DV162923.1|DV162923

EST:     CCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAG                         AAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA
genomic: CCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattg ... ttgataacagAAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCA

EST: gi|211447144|gb|FL470093.1|FL470093

EST:     CAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATG-TCACANGG                         AAG-AACACACAAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGG
genomic: CAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACA-AGgtaaacattg ... ttgataacagAAGAAACACAC-AAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGG

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: 65

TGATGACATGATTGCTGTAAATAATATGCGTTGCTTATGTGGGCCTGATACCAAAAAGTCTTCAGTAGGGGGTTTTACACTGAAATTTGATGTTCACAAGgtaaacattg ... ttgataacagAAGAAACACACAAATCGAAAAGAGCGAACAGGGGAAGAATCAACATGGGCACTCTCTCGATTTTACCCTATTTTGGAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 98