ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagcaatctagtacttgttagcttttcttagaggtccgctagttactagactccatcttaaataatcaatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAACAAAGCATATCTACCAGAGACCATCTGGTTGATCTGTCATAAACCTGCAA

Basic information

species	Zea mays
transcript	GRMZM2G100707_T01
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 13

gtaagcaatctagtacttgttagcttttcttagaggtccgctagttactagactc--------catcttaaataatcaatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAACAAAGCATATCTACCAGAGACCATCTGGTTGATCTGTCATAAACCTGCAA--
       || || |  || |    ||||   ||||||| ||||   |||||  ||        |||  | |  | | ||  |||||||||||| || ||||||||||||||||||||||||||  ||||||| |||||||||||| ||||||| |||||||| |||||||   | |||  ||||| |  
-----gtatgtaatgtttctagaatttta--agaggtctgctataaactagggtcaatactgacattctgacaattaaactctgcagGCATGATCTCGAAGTGAATGGTGGAAAGGGCATAATAATTGACCCTAGAACAAAGCATGTCTACCAAAGACCATCAGGTTGATAAAT-ATAG-CCTGCTATA

upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 14

gtaag--caatctagtacttgt-------tagcttttcttagaggtccgctagttac-tagactccatcttaaataatcaatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAACAAAGCATATCTACCAGAGACCATCTGGTTGATCTGTCATAAACCTGCAA---
|||||  || |||| | ||          || | ||  | ||   ||   | |||      |||  | |||   | |  |||  ||||||||||| |||||||| || || ||||| ||  ||||||||||||||||||||||  |  | || ||  | ||||       |    ||| | |||   |    
gtaagttcactctactcctcacactctagtaacgttattcagttctcgatttgttttacttactagaccttgtgtgaaaaat--tgcagGCATGATCTTGAAGTTAACGGAGGAAAAGGTCTAATCGTTGACCCAAGAACAAAATACGTTTATCAACGGCCATGAACCAAA---ATCAAAGACCGTTACTTT

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|93015870|gb|EB641390.1|EB641390

EST:     TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGG
genomic: TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGG

EST: gi|32936928|gb|CF041747.1|CF041747

EST:     ATTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: ATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

EST: gi|211442681|gb|FL456308.1|FL456308

EST:     TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

EST: gi|37398356|gb|CF636490.1|CF636490

EST:     TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

EST: gi|5915101|gb|AW052742.1|AW052742

EST:     TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTCTTCCA                         GCATGACCTTGAAGTGAATGGNGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

EST: gi|149097072|gb|EE182879.2|EE182879

EST:     TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

EST: gi|4630578|gb|AI621452.1|AI621452

EST:     TTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: TTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

EST: gi|211221036|gb|FL467849.1|FL467849

EST:     TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA                         GCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC
genomic: TTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAAC

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: 47 (upstream exon), 47 (downstream exon)
Score: 65

GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCAgtaagcaatc ... aatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAACAAAGCATATCTACCAGAGACCATCTGGTTGATCTGTCATAAACCTGCAA

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 56

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

Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 52

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttagaggtccgctagttactagactccatcttaaataatcaatcctgcagGCATGACCTTGAAGTGAATGGTGGAAAGGGCATAATCGTTGACCCAAGAACAAAGCATATCTACCAGAGACCATCTGGTTGATCTGTCATAAACCTGCAA