ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGATTCAGTCGGTTTTCGGATTATCTGATGGATCTGGCTTGGCTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaagcatagcaattggcctaaaaacagaatttggtgccacttatgattttagctgtttctgagtagttgtgaatgatatttttttag

Basic information

species	Zea mays
transcript	GRMZM2G379002_T01
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G379002_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g57060.1 (Oryza sativa), 5'ss of exon 10

GAAGATTCAGTCGGTTTTCGGATTATCTGATGGATCTGGCTTGGCTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaag-agtaagca-tagcaattggcctaaaaacagaattt-------ggtgccacttatgat-------------------tttagctgtttctgagtagt--tgtgaatga--tatttttttag
|||||| || ||||| || |  ||||||||||| |||||||| ||||| ||||| || |||||||||||||| || ||||| ||||| |||||||| || | |  ||| |||||    | | |     | |||||       |  | ||  | ||||                   |||| ||     ||  |  |  ||| || |   || |||| |||
GAAGATCCAATCGGTGTTTGCGTTATCTGATGGCTCTGGCTTAGCTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattgcgcaatagcagcatgtcaatggcgaaaattttcgtcaggaaggcaagtgtgatcaaggaaaacgaacccttttttaactccagttgcttgatcctgtaaacgctttacttttgtag

upper sequence: GRMZM2G379002_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA20G34110.1 (Glycine max), 5'ss of exon 13

GAAGATTCAGTCGGTTTTCGGATTATCTGATGGATCTGGCTTGGCTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaagcatagcaattggcctaaaaacagaatttggtgccacttatgattttagctgtttctgagtagttgtgaatgatatttttttag
|||||| || || ||||| |   | |||||||| ||||| |||| |||||| || || ||||| || || ||||||||||| || |||||||||||     |   | |     |   |||   ||     ||| || || || |        |   |||    ||||                     
GAAGATCCAATCAGTTTTTGAGCTCTCTGATGGCTCTGGATTGGTTGTTACTGTTGCTCGCTACGAGACACCTGCACATACAGATATTGACAAGgtt----tgctcttgattctccacctcctaaactggtttcgt-ccgctaacaccc---ggcatttgcatgtag---------------------

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|18650354|gb|BM499173.1|BM499173

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|13237335|gb|BG355349.1|BG355349

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|32849775|gb|CD989456.1|CD989456

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|13557805|gb|BG549161.1|BG549161

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|13237129|gb|BG355143.1|BG355143

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|13249969|gb|BG360874.1|BG360874

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTGCCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|16378625|gb|BI992526.1|BI992526

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGTCCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|149008586|gb|EE040765.2|EE040765

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|211093591|gb|FL440788.1|FL440788

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

EST: gi|161407607|gb|DW042452.1|DW042452

EST:     CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAG                         GTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA
genomic: CTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 14

GAAGATTCAGTCGGTTTTCGGATTATCTGATGGATCTGGCTTGGCTGTTACCGTAGCACGCTATGAAACTCCTGCACATACCGACATTGACAAGgtaagagtaa ... atttttttagGTTGGTGTGATTCCAGACCGACCACTGCCAGCTTCATTTCCTACCGATGAAGATGCCTTCTGCAGCTGCCTTAGGGATTCAACGGCTGCTTGCAATCTGA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 29

Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 46