ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGATAAAATAATTGGTTTTGCTTTGAGCCATCAACTTAAGAACTGTACAAATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAGgtttcaaatctattctagtgcttcaatttttctataagattacttctcaacagaaatgcttatttgttccactgttaccattacag

Basic information

species	Zea mays
transcript	GRMZM2G042074_T02
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g22420.2 (Oryza sativa), 5'ss of exon 19

---TTGATAAAATAATTGGTTTTGCTTTGAGCCATCAACTTAAGAACTGTACAAATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAGgtt---tcaaatctattctagtgcttcaatttttctataagattacttctcaacagaaatgcttatttgttccactgttaccattacag
   ||||||||||| |||||||||||||||| |||||||||||| ||| ||||| |||||||||   || |||| |||| |  ||   |||||| || ||||||||   || ||||| |  |  | || ||   |  | | ||  || ||  | | |          || |||   | |||  ||| | |||
GTATTGATAAAATAGTTGGTTTTGCTTTGAGTCATCAACTTAAGCACTCTACAATTCCAGACCC---TTCGAGTGATGTTCGTTTCACTCTATCTAGTGAAAGgttcactctaatctttatttcttctccacaatgccaacaaagtt-ctctttatccagtgcatcaatgtgtat-attgt--ccactgcag

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|67017525|gb|CO446274.1|CO446274

EST:     AATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAG                         CCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAG
genomic: AATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAGgtttcaaatc ... accattacagCCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAG

EST: gi|67033220|gb|CO461969.1|CO461969

EST:     AATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGGTCTATCCAGCGAAAG                         CCTTAAGCATGGTGTTGACATGTTGGNAAGTATCCAGTCTGGCTCGAAGAG
genomic: AATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAGgtttcaaatc ... accattacagCCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAG

EST: gi|31359802|gb|CD444159.1|CD444159

EST:     AATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAG                         CCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAG
genomic: AATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAGgtttcaaatc ... accattacagCCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 135

TTGATAAAATAATTGGTTTTGCTTTGAGCCATCAACTTAAGAACTGTACAAATCCAGACCCCCCTTTGAGTAATGTGCAGTTTGTTCTATCCAGCGAAAGgtttcaaatc ... accattacagCCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178