ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattcaaatgtcgagcacgccatttgtctccaacgagacaacgatgtagatgcttagactctttgatgtgccatgttgtgcacatttgaaccttatcaattcttcctcatatgtgtag

Basic information

species	Zea mays
transcript	GRMZM2G128771_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G128771_T01 (Zea mays), 5'ss of exon 5
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 5'ss of exon 6

ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattcaaatgtcgagcacgccatttgtctccaacgagacaacgatgtaga-tgcttagactctttgatgtgccatgttgtgca-catttgaaccttatcaattcttcctcatatgtgtag
 ||||||||||  || || || ||    |||||    ||  |||| || |  ||||| |||||||||||||| || ||| |||||||||||||  |    | ||| |     || ||   || |   | | | |   | |  ||  |||    | |||    ||     |    | |  |||  |  | |   |                     
GCAAGTGTCCATTGAGGAGGGCGACGCAAAGGCGCGGGAGCTGAACGTGAACTTCATTGAGACCAGCGCGAAGGCTGGCCTCAACATCAAGgt-gggcggatatgcctc-ttcgtcagg-gtttgggatggggcggagctccaggctgcacgcattctgcactgcaatgtaaccttcggcatgcgggcttgtgc---------------------

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|149095335|gb|EE180972.2|EE180972

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|37387848|gb|CF631126.1|CF631126

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|211492535|gb|FL462462.1|FL462462

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|211435904|gb|FL357606.1|FL357606

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|37379915|gb|CF626729.1|CF626729

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|40335969|gb|CK370039.1|CK370039

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|211481374|gb|FL368109.1|FL368109

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCTAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

EST: gi|211492534|gb|FL462461.1|FL462461

EST:     TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAG                         CCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA
genomic: TGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCA

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: 28 (upstream exon), 43 (downstream exon)
Score: 4

ACAAGTGTCCACAGAAGAAGGAGAGAGCAAGGCAAAAGAATTGAATGTCATGTTCATCGAGACCAGCGCGAAAGCCGGCTTCAACATCAAGgtcagattca ... atatgtgtagCCGTTGTTCCGCAAGATCGCTGCAGCCCTGCCAGGAATGGAGACATTGTCAGCAAAGCAGGAGGACATGGTGGATGTCAACCTGAAGTCGACTTCTAGCC

Block sizes: 28 (upstream exon), 26 (downstream exon)
Score: 7

Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 5