ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCGGCGCAGGAGCAGCAGGCCAACGGCAACGGCGAGCAGAAGACGCGGCACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactccgatcctgcctgcccatttccggcctcgcgctctagatcttatcttccgtgactcgaatctgaccgggggaagaatcacttccaccag

Basic information

species	Zea mays
transcript	GRMZM2G127948_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g06980.2 (Oryza sativa), 5'ss of exon 1

GCCGGCGCAGGAGCAGCAGGCCAACGGCAACGGCGAGCAGAAGACGCGGCACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactccgatcctgcctgcccatttccg-------gcctcgcgctctagatcttatcttccgtgactcgaatctgaccgggggaagaatcacttccaccag
| || || || ||  | | |  | | ||  |||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||||||| |   |   ||| |||  ||| |   ||        ||||   | |     || | ||| | ||||| |   |||||  || |     ||  |||| |   
GACGACGGAGCAGGCGAATGGGAGCAGCGGCGGCGAGCAGAAGACGCGGCACTCGGAGGTCGGCCACAAGAGCCTCCTCAAGAGCGACGATCTCTACCAGgtaacccgccgtctccggccatcccctcctcgccggaaaacctccgccgccgtggctgaccttgcctgactgg---ctgactcggtgct---tcgtttccgcag-

upper sequence: GRMZM2G127948_T04 (Zea mays), 5'ss of exon 3
lower sequence: EFJ35623 (Selaginella moellendorffii), 5'ss of exon 1

GCCGGCGCAGGAGCAGCAGGCCAACGGCAACGGCGAGCAGAAGACGCG-GCACTCCGAGGTC--GGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactccgatcctgcctgcccatttccggcctcgcgctctagatcttatcttccgtgactcgaatctgaccgggggaagaatcacttccaccag
    ||  | | |       | || ||||| |   || |  |  |  |   || || |  ||  |||||||||||||| |||||||||||||  ||||| ||||||     ||| |   |      |||  |   ||   |  |||||||| ||  || |  |||| |                                 
---TGCAAACGGGAGTTCTTCTAATGGCAAAGCAAAGGAAGAAGCTAGCAAACACCAAACTCTTGGCCACAAGAGCCTCCTCAAGAGCGACGCTCTCTATCAGgtac---ttccaagttt------ccaaat---gctctgatctctagatttt--ctccattgacgcag-------------------------------

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|18659584|gb|BM500414.1|BM500414

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211221107|gb|FL365189.1|FL365189

EST:     TCCAGAGGTCGCGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: TCC-GAGGTCG-GCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211388332|gb|FL320898.1|FL320898

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211460076|gb|FL334958.1|FL334958

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211015370|gb|FL327151.1|FL327151

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211359692|gb|FL340690.1|FL340690

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211200543|gb|FL334723.1|FL334723

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|149076214|gb|EE164811.2|EE164811

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|148967413|gb|EE018639.2|EE018639

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCCGCGGGAGCCGGAGAGCATGAAGGA
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCC-GCGGGAGCCGGAGAGCATGAAGGA

EST: gi|74233832|gb|DT641746.1|DT641746

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

EST: gi|211147965|gb|FL321980.1|FL321980

EST:     ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAG                         TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG
genomic: ACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAG

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), 49 (downstream exon)
Score: 200

GCCGGCGCAGGAGCAGCAGGCCAACGGCAACGGCGAGCAGAAGACGCGGCACTCCGAGGTCGGCCACAAGAGCCTGCTCAAGAGCGACGACCTCTACCAGgtaaacactc ... cttccaccagTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 588

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 608