ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCATGGTGGATCACGTGCTGCTGAGTATTTGAGGGAGCACTTGTTTGAGAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttctcttcagctgtactgtagacttcctgttgccattattgttggtgctacaacctgtttatctgctaaacttgaatttaaaacag

Basic information

species	Zea mays
transcript	GRMZM2G442404_T04
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G442404_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g15594.1 (Oryza sativa), 5'ss of exon 3

GTCATGGTGGATCACGTGCTGCTGAGTATTTGAGGGAGCACTTGTTTGAGAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttctcttcagctgta----ctgtagacttcctgttgccattattgttggtgctacaacctgtt--tatctgctaaactt--gaatttaaaacag--------------
||||||| ||| ||||||||||||||||||||| |||  | ||||| || || ||||| || |||||||| ||| |||| |||||||||||||| ||||||| || |||||||    | |      |  ||   ||   |  || || || |    | | | |    ||  ||||| || |||||  |||   ||||                 
GTCATGGAGGACCACGTGCTGCTGAGTATTTGAAGGAAAATTTGTTCGAAAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttctctttgattcttacctttccagttctctgttcaccttttttttaaaggttgctaatgattattatcttctcaacttttgaaaaaaaaatcaaaacataacaacag

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|78179208|gb|DV549581.1|DV549581

EST:     GAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAA                         GCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG
genomic: GAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttc ... tttaaaacagGCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG

EST: gi|71428856|gb|DR809906.1|DR809906

EST:     AAGCTTGCTATAA                         GCGAAACATTTCAAAAAACCGATACAGATTT-TTGGAATCGGAAGCAAGTG
genomic: AAGCTTGCTATAAgtatttcttc ... tttaaaacagGCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG

EST: gi|32931838|gb|CF036650.1|CF036650

EST:     GAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAA                         GCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG
genomic: GAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttc ... tttaaaacagGCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG

EST: gi|8103065|gb|AW927729.1|AW927729

EST:     GAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAA                         GCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG
genomic: GAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttc ... tttaaaacagGCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTG

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), 46 (downstream exon)
Score: 176

GTCATGGTGGATCACGTGCTGCTGAGTATTTGAGGGAGCACTTGTTTGAGAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttc ... tttaaaacagGCGAAACATATCAGAAAACCGATACAGATTTCTTGGAATCGGAAGCAAGTGCTTTCAGAGATGATGGTTCAACAGCTTCAACTGCAATTTTGGTGGGTGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129