ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttctagatgcttttttaaccttttgacctctgtgtttttaacatgattgtaaagagtatttttctttataaacataaatcacttggacagttg...

Basic information

species	Zea mays
transcript	GRMZM2G308570_T02
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G308570_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G35010.1 (Glycine max), 5'ss of exon 2

GCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttctagatgcttttttaaccttttgacctctgtgtttttaacatgattgtaaagagtatttttctttata--aacataaatcacttggacagttg---
|||||| || || || || || || ||| | || ||||||||||| |||||||| ||||||||||| || |||||| || ||||  ||| |     |||  ||| ||     |    | || |  ||| || |      |       ||    |||| |  |   ||      |||     |||   
GCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGGgtgggttgt-----tgcactttcaaatagatattatgtgggcattttacctctccagagcttaagttgcaatttaaattagtgtagcatgtttgtgttcttgcca

upper sequence: GRMZM2G308570_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G02860.1 (Glycine max), 5'ss of exon 3

GCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttctagatgcttttttaaccttttgacctctgtgtttttaacatgattgtaaagagtatttttctttataaacataaatcacttggacagttg---
|||||| || || || || || || ||| | || ||||||||||| |||||||| ||||||||||| || |||||| || ||||  ||| |     |      |  |  || ||    |  | | | |  |  || | | |   | | |||  |||   |   | |     |||     |||   
GCCTCAGGTAACTATAGCAACGGCCATAATCTTTTGTCATCGGTTCTTTCTTCGACAATCTCATGCAAAGAATGACCGAAGGgtgggttgttgcactttcaaatagatattatgtaggcattttgtctctccagagtttgagttgcaatttaattt---agtgtgatatgtttgtgttcttgcca

upper sequence: GRMZM2G308570_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT4G19560.1 (Arabidopsis thaliana), 5'ss of exon 3

GCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttctagatgcttttttaaccttttgacctctgtgtttttaacatgattgtaaagagtatttttctttataaacataaatcacttggacagttg---
 || || || ||||| || ||||||||| | |||||||| || || || ||||||||||| ||||||||||||||||||| ||| |||||    | ||  | |  ||   |     ||  |    | ||      || |     ||  ||||   |  ||  || | ||  || |     ||   
TCCCCAGGTAACAATAGCCACTGCTATATTTTTCTGTCACCGATTCTTCCTTCGTCAATCACATGCGAAAAATGACAGACAGgtgagttt---ggttggatgtgaaaaaatggtcactaaggaagtatatgtcttttttcctctgttgttttgagtgaaactatgagtctattagctgtctggtg

upper sequence: GRMZM2G308570_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S119_132V6.2 (Physcomitrella patens), 5'ss of exon 4

GCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttctagatgcttttttaaccttttgacctctgtgtttttaac-atgattgtaaaga-gtattttt-ctttataaac--ataaatcacttg-gacagttg-------------------------------------
 || |||||||| ||||| ||||| || || ||||| ||||||||||| | ||| ||||| ||||| |||||||||||||  || ||| | ||  | ||  |     |||  | |  |  ||      ||   ||||  ||   | ||| |    ||||    |    | ||  | |||  ||  ||                                      
TCCCCAAGTGACTATTGCAACTGCCATTGTATTCTGCCATCGGTTTTTCCATCGACAATCACATGCAAAAAATGACAGACTTgtgagtat-ctgcaagccctggattcctccttatttaggtccagggaattgtgatcctaggcatgtactacagctttgcggatttgtgaacaatttgtaacttttatttgttcttgtgctcatgagtatgtgtatttttacag

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|76937118|gb|DV175047.1|DV175047

EST:     TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG                         ACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC
genomic: TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttc ... aacaatgcagACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC

EST: gi|93283332|gb|EB675596.1|EB675596

EST:     TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG                         ACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC
genomic: TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttc ... aacaatgcagACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC

EST: gi|78111792|gb|DV530189.1|DV530189

EST:     TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG                         ACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC
genomic: TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttc ... aacaatgcagACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC

EST: gi|149102056|gb|EE287526.2|EE287526

EST:     TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGG                         ACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC
genomic: TCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttc ... aacaatgcagACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCC

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), 45 (downstream exon)
Score: 141

GCCTCAAGTGACAATTGCTACTGCTATAGTGTTCTGTCATCGGTTTTTTCTTCGTCAATCTCATGCGAAAAATGACAGACGGgtaagttttc ... aacaatgcagACAATTGCAACAGTATGTATGTTCTTGGCGGGAAAAGTTGAAGAAACACCCAGACCTCTGAAGGATGTCATACTTCTTTCATACGAGATCATCCACAAAA

Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 96

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 111