ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGTGATAGCTTTCTTTTACTGGACATCTAATTTTCATCGTTTCGAATTCTTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgcatttcatctggtactggtttactgtttggcattattattctaccataaagtactccagtattgttatattttaattttactgttgtgtgtt...

Basic information

species	Zea mays
transcript	GRMZM2G079428_T02
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G079428_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g34400.2 (Oryza sativa), 5'ss of exon 11

---CTGTGATAGCTTTCTTTTACTGGACATCTAATTTTCATCGTTTCGAATTCTTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgcatttcatctggtactggtttactgtttggcattattattctaccataaagtactccagtattgttatattttaattttactgttgtgtgtt-
   |||||||||||||||||||||||||||| || ||||||| ||| ||||||||||| ||||||| ||||||||| ||||| |     | ||  |||| |||||||| || ||||  |||     |||   |    ||    |  | |    | | | |  |  || | | | |    || ||    || || |  |   || 
GTCCTGTGATAGCTTTCTTTTACTGGACATCAAACTTTCATCTTTTTGAATTCTTTAGGCGGTTGAAGCTTCCTGATTAGTTTCAG---AGAATCAGTTGAAGgtaaa-tgaattttgtctttgtgtggcccagctgttattgtgctgaagtaatcttcatatgttctattctcgcaccatattgcacttgctatgtttaatta

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|60354927|gb|DN221900.1|DN221900

EST:     TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAG                         GAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC
genomic: TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgca ... gagccaacagGAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC

EST: gi|7135406|gb|AW498070.1|AW498070

EST:     TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAG                         GAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC
genomic: TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgca ... gagccaacagGAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC

EST: gi|211222234|gb|FL086602.1|FL086602

EST:     TAGACGGTTGAGGCTTCCCTGAATAGTTCCCCATCTAAAAGTAGTTAAAG                         GAGTTGCCCTGGGATTACATTTTTCCGAGGACAGAATTCTGATGTGAAGAG
genomic: TAGACGGTTGAGGCTTCC-TGAATAGTTCCC-ATCTAAAAGTAGTTAAAGgtaaactgca ... gagccaacagGAGTTGCC-TGGCATTACATTTT-CCGAGGACAGA-TTCTGATGTGAAGAG

EST: gi|60352111|gb|DN219084.1|DN219084

EST:     TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAG                         GAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC
genomic: TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgca ... gagccaacagGAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC

EST: gi|7135032|gb|AW497882.1|AW497882

EST:     TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAG                         GAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC
genomic: TTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgca ... gagccaacagGAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGC

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: 33 (upstream exon), 49 (downstream exon)
Score: 40

CTGTGATAGCTTTCTTTTACTGGACATCTAATTTTCATCGTTTCGAATTCTTTAGACGGTTGAGGCTTCCTGAATAGTTCCCATCTAAAAGTAGTTAAAGgtaaactgca ... gagccaacagGAGTTGCCTGGCATTACATTTTCCGAGGACAGATTCTGATGTGAAGAGGGCGCCTGGCATGAATCAAGGGGCATCTCCACCCACTCTGAAAGGCTGCCAT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 37