ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcctgtctgtatagtaaacgtgaacctgtaccatgatatatctcattcttattttctgcatttgttactactttag

Basic information

species	Zea mays
transcript	GRMZM2G179421_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G179421_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g21940.1 (Oryza sativa), 5'ss of exon 10

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagt-----cctgtctgtatagtaaacgtgaacctgtaccatgatatatctcattcttattttctgcatttgttactactttag
||||||| |||||||||| ||||||||||||||||| ||| ||||||||| |||||||||||||||||||||||| ||| |||| ||||| || ||||||||| |  |     ||  | | | | |||    | ||| || ||    ||     | |   |  | ||    || ||  |||  | |||
ACTGAAAAATGAGAATCTTTCTCCTCTTCTTCCCCTGGACATCAATCTAATTGACCCATCACTCAGTGGTTTGGAGAGGGCATTATCACAGCTTGATATGgtatgcatgtctccccctttctgttgtaccattaaacatgaactggcatggcatttaccttattcttgctaatatggcact-ttctag

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|22545689|gb|BU098048.1|BU098048

EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|26558065|gb|CA830300.1|CA830300

EST:     TGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGN
genomic: TGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|120479870|gb|EH210656.1|EH210656

EST:     AAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: AAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|211190020|gb|FL186110.1|FL186110

EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCACTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|32945711|gb|CF050530.1|CF050530

EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|60343676|gb|DN210649.1|DN210649

EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|32936531|gb|CF041350.1|CF041350

EST:     CATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|78021778|gb|DV490165.1|DV490165

EST:     CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGT

EST: gi|211190018|gb|FL186108.1|FL186108

EST:     CTGACCCATCACTCARTGGTTTGGAAAGGACATTGTCACAACTCGATATG                         GCAAATGAGCAT
genomic: CTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCAT

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), 48 (downstream exon)
Score: 189

ACTGAAAGATGAGAATCTGTCTCCTCTTCTTCCCCTAGACGTCAATCTAACTGACCCATCACTCAGTGGTTTGGAAAGGACATTGTCACAACTCGATATGgtacgagtcc ... actactttagGCAAATGAGCATTTGCAAAGTATTTTTCCATCATTTAAAGAGCTTCCTGGTTCTGGCAATGCTTTGGAAAGATTACTCGCCTTGGAACTCGAGCTTGCAG

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 84

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100