ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACCGGGTTGAATTCATCAAACCTGAGGAGGCAGCTCATTTGGAGAGAAACTTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgccactattcgctacatctgcaataatggccatttgaaggcccccaaggttttggagttcgaactaatgtcgaaaattatgtgcctatttag

Basic information

species	Zea mays
transcript	AC217947.4_FGT002
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 5'ss of exon 7

ACCGGGTTGAATTCATCAAACCTGAGGAGGCAGCTCATTTGGAGAGAAACTTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgccactattcgctacatctgcaataatggccatttgaaggcccccaaggttttggagttcgaactaatgtcgaaaat-tatgtgcctatttag---------
|||||||||||||  | || ||||| |||||||| |||||||||||||| ||||| |||||||| ||  |||| || |||||||| ||||||||||||| ||||| ||||  ||||    | ||| ||   |  |     | ||   | |   |   || |   | | |||   | |   | ||| |       | ||| |         
ACCGGGTTGAATTTGTTAAGCCTGATGAGGCAGCCCATTTGGAGAGAAATTTCAGTCTTGCAAACGGTTATGCGGTTCATGATGCTCAGCATCCTTGCCGgtaagtatgcggctataaagtccatttgttttcttaatagtatggttgtctgtat--ttgtaatggtggaatcgaagctaacaatctgcaaatttcttttgaatctgtag

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|108953570|gb|EC364784.1|EC364784

EST:     CAGCCTTGCAAATAGCCATGCAAGTCCATGATGCCCAGACATCCTTGCCA                         GGCTTAATGTGGTCGTGCGGCAGGAAC
genomic: CAGCCTTGCAAATGGCCATGCA-GTCCATGATGCCCAG-CATCCTTGCCAgtaagaatgc ... gcctatttagGGCT-AATGTGGTCGTGCGGCAGGAAC

EST: gi|148961292|gb|EE012017.2|EE012017

EST:     TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCA                         GGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC
genomic: TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgc ... gcctatttagGGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC

EST: gi|38502682|gb|CF972542.1|CF972542

EST:     TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCA                         GGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC
genomic: TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgc ... gcctatttagGGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC

EST: gi|74235808|gb|DT643722.1|DT643722

EST:     TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCA                         GGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC
genomic: TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgc ... gcctatttagGGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC

EST: gi|13149591|gb|BG319913.1|BG319913

EST:     TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCA                         GGCTAATGTGGCCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC
genomic: TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgc ... gcctatttagGGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC

EST: gi|74235807|gb|DT643721.1|DT643721

EST:     TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCA                         GGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC
genomic: TTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgc ... gcctatttagGGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTC

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), 47 (downstream exon)
Score: 52

ACCGGGTTGAATTCATCAAACCTGAGGAGGCAGCTCATTTGGAGAGAAACTTCAGCCTTGCAAATGGCCATGCAGTCCATGATGCCCAGCATCCTTGCCAgtaagaatgc ... gcctatttagGGCTAATGTGGTCGTGCGGCAGGAACTCCACACCCCTGCTTCTGATCGTTCATGCACTCATTTGGAGTTCGACATTGCTGCAACTGGTCTCAC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 310

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197