ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagacagtgcagtagctaaacagtttatccttcttgactgcttctaatttcataggtgaatactgaatagtgaaaattagaaatgtatttttgtactcttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG

Basic information

species	Zea mays
transcript	GRMZM2G127717_T01
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127717_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 11

gtaa--gacagtgca-gtagctaaacagtttatccttcttgactgcttctaat-ttcat--aggtgaat--actgaatag-tgaaaattagaaatgtatttttgtactc-ttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG
||||  | ||||||  |  |    |  ||||  |     ||| |||| | |||  ||||  |  | | |  | | ||| | || ||||| ||  || ||| ||| | |  ||    |||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||||
gtaataggcagtgcgtggtgtcttagggttttgcacagatgagtgctacaaatactcatacaactcattgaattaaatggatggaaatttgat-tggattcttggatttgttcttgcagGATTTACTGCAAAAATCAAATGCAACTGATGCATCAGGAAATGTAATACTTAGTGACTTTGGTGTCCACATGCAACAGAAG

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|71432245|gb|DR813295.1|DR813295

EST:     TTAATACAAAGGGATTTTGTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAG                         GATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTT
genomic: TTAATACAAAGGGATTTTGTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaagacagt ... cttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTT

EST: gi|56382617|gb|CV985286.1|CV985286

EST:     TTAATACAAAGGGATTTTGTGTGGTTTGTGTTGTTGAAGGTGCAGGGCAG                         GATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTT
genomic: TTAATACAAAGGGATTTTGTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaagacagt ... cttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTT

EST: gi|166551792|gb|EG159192.1|EG159192

EST:     TTAATACAAAGGGATTTTGTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAG                         GATTTACTGCAAAAATC
genomic: TTAATACAAAGGGATTTTGTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaagacagt ... cttggcacagGATTTACTGCAAAAATC

EST: gi|211225796|gb|FL287050.1|FL287050

EST:     TA-TACAAAGGGATTTTTGTGTGGTTTGTGNTGCTGAAGGTGCAGGGCAN                         GATTTACTGCAAAAATTCAA-TGCNACTGACGCTTCAGGAAATGTGGATAC
genomic: TAATACAAAGGGATTTT-GTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaagacagt ... cttggcacagGATTTACTGCAAAAAT-CAAATGCAACTGACGCTTCAGGAAATGTG-ATAC

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), 47 (downstream exon)
Score: 41

CTTCACACTTGATGGAGAACATGGTGTCTTGCGACACCTTGAGCATTTACTTAATACAAAGGGATTTTGTGTGGTTTGTGTTGCTGAAGGTGCAGGGCAGgtaagacagt ... cttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 34

Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 16

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 19

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taggtgaatactgaatagtgaaaattagaaatgtatttttgtactcttggcacagGATTTACTGCAAAAATCAAATGCAACTGACGCTTCAGGAAATGTGATACTTAGTGACTTTGGTGTCCACATGCAGCAGAAG