ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTGGACGCTGTTCTTTGCTGGTGTCACGGCTGTTGGATTTGGTTCTTCCTATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttccttttcttactttgccttatgttccatggagttcatagtttctacttgtgtttactcctaaggagtcccatagtcgtatgctatttaccagc...

Basic information

species	Zea mays
transcript	GRMZM2G147709_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147709_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g73120.1 (Oryza sativa), 5'ss of exon 3

TTGGACGCTGTTCTTTGCTGGTGTCACGGCTGTTGGATTTGGTTCTTCCTATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcctttt---cttactttgccttatgttccatggagttcatagtttctacttgtgtttactc---ctaaggagtcccatagtcgtatgctatttaccagc
|||||| ||||||||||||||||| || |||||||  |||||||| ||||||||||||||||| |||||||| ||||| ||||||||||||||| |||| |||||||  || |   ||||| |||||||  | || | |   |  | |    | | || |||| |  |   || || |   | ||      ||  | |||      
TTGGACACTGTTCTTTGCTGGTGTGACTGCTGTTGCTTTTGGTTCATCCTATTATCATCTCAAACCGAATGATGCCACACTAGTTTGGGACAGATTGCCGgtgagttgtttctagacttacattgcctt--gctctaggatttgtacacacccca-ttatgttgaagctgtctcagaatgtcaatgcatacattttttttggt---

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|60352475|gb|DN219448.1|DN219448

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT

EST: gi|211218284|gb|FL207814.1|FL207814

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCAC
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCAC

EST: gi|211515170|gb|FL354450.1|FL354450

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGC
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGC

EST: gi|211166571|gb|FK969119.1|FK969119

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGGT
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT

EST: gi|67012775|gb|CO441524.1|CO441524

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT

EST: gi|211049503|gb|FL332054.1|FL332054

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCA
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCA

EST: gi|12046333|gb|BF728472.1|BF728472

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT

EST: gi|12045665|gb|BF727804.1|BF727804

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT

EST: gi|78180036|gb|DV550409.1|DV550409

EST:     ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCA                         ATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT
genomic: ATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTT

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: 42 (upstream exon), 44 (downstream exon)
Score: 27

TTGGACGCTGTTCTTTGCTGGTGTCACGGCTGTTGGATTTGGTTCTTCCTATTATCATCTCAACCCGAATGACGCCACCCTAGTTTGGGACAGACTGCCAgtgagttcct ... ttttttctagATGACGATTGCTTTCACTTCTGTCATGGCTATATTCATTATTGAAAGGGTTGATGATAGAGCAGGGGCAAAATCCCTTGCACCACTTGTGATTGCGGGTG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 57

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 61