ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGGAATAGCTTGTGGAAATCCAAGAGGGATGAACAACGCCCATTAAGATATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgatttcctctgctgcaccacactattctagatttaagatgtttatatgtaatatgatcttattgagagtaacttattggatatatgtgtgtgc...

Basic information

species	Zea mays
transcript	GRMZM2G112782_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112782_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g14640.1 (Oryza sativa), 5'ss of exon 3

TTGGAATAGCTTGTGGAAATCCAAGAGGGATGAACAACGCCCATTAAGATATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgatttcctctgctgcaccacactattctagatttaagatgtttatatgtaa-----tatgatcttattgagagtaacttattggatatatgtgtgtgc
  ||||||||||||||||| ||||||| |||||||| |  || ||||||||||||||| || || |  | |||   |||||| || |||||||| |||||||||| | | |  | ||||||        |||| |||||  ||||  |  | |  |||           |    ||      | ||| | | ||  | ||     
GAGGAATAGCTTGTGGAAAGCCAAGAGTGATGAACATCTTCCGTTAAGATATGATATGCCAAATCACTTAGACTGGAGGGTTATAACCTTATTAGCACAGgtataactactaaccctgctgagaggagttattgtagatgaaagaattaaagaaataaaccccccccccccccctgttttgcatttacttggtacctttg-----

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|60359241|gb|DN226214.1|DN226214

EST:     ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|110194413|gb|EC876311.1|EC876311

EST:     ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|149070488|gb|EE158891.2|EE158891

EST:     ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|71442014|gb|DR823064.1|DR823064

EST:     ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|14204198|gb|BG837875.1|BG837875

EST:     ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|110193128|gb|EC875026.1|EC875026

EST:     TGATATGTCATATAATCTTGGCCTCAGGGGTTGTATCCTTTTTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: TGATATGTCATATAATCTTGACCTCA-GGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|60337811|gb|DN204784.1|DN204784

EST:     CTTGACCTCAGGGTTGTATCTTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: CTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

EST: gi|211054682|gb|FL184554.1|FL184554

EST:     ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAG                         AGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG
genomic: ATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAG

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: 96

TTGGAATAGCTTGTGGAAATCCAAGAGGGATGAACAACGCCCATTAAGATATGATATGTCATATAATCTTGACCTCAGGGTTGTATCCTTATTAACACAGgtatatcgat ... cgttttacagAGATTTAATGGGCTAGCGGAGAGAAGCAGAAATTATTTGACAAGTTGGAAGGAAAATTCCAGGACTTCTGGAAGGACGGGTGGGCTTCATATACAAGGCC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 37

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27