ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgttattgtttattgcaacttttataagtacacattaatctattttccagattctcatcatattatattctgagtgtctgatag

Basic information

species	Zea mays
transcript	GRMZM2G078576_T04
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 14

GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgttattg--tttattgc---aacttt------tataagtacacattaatctatt-----ttccagattctcatcatattatattctgag--tgtctgatag
|| || |||||| | ||||||||||||||||| ||| ||||||| ||||| ||||| || || |||||| |||||||||| || ||||| |||||||||||||  ||| || |   |||||       || || |||| | ||||| | |     ||||        |||  |  || || |||   ||||||  ||
GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaag

upper sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA20G28880.1 (Glycine max), 5'ss of exon 13

GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgttat---tgtttattgcaacttt---tataagtacacattaatctatt-----ttccagattctcatcatattatattctgagtgtctgatag--------------------------------------------------------------------------------
|| || |||||  || ||||  | || || || ||| ||||||| || |||||||||||||| ||||||||| |||| ||||| || ||||||||||| ||   |||||  |  || |     ||  |  | |   | | |  ||      |    | | | |    |  |  || || |       |||                                                                                
GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACTgtatgtgtcatatatgttttatttaaatgaaagtaccaaaatatgctgaccctttgcaatcttgtaacttttaaaggagcaagttttgtgctatctttagtcacattaatgaagcttgtctttgtataataaatcatgtttctcaagtgtgtgcaaaatgtatctattaaatatttacag

upper sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G38920.2 (Glycine max), 5'ss of exon 14

GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgttattgtttattgcaacttttataagtacacattaatctattttccagattctcatcatattatattctgagtgtctgatag------------
|| || |||||  || ||||  | || || || ||| ||||||| || ||||||||||| || ||||||||| |||| ||||| || ||||||||||| ||   |  ||   |  |||| | | | |  || ||    ||     |   |    | |||   | || |   | | |||             
GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGCTTCAATGAACTGATTGATAACATTTATACTgtatgtgtcatatatattttttaggtttaaatgca-attttgattcccttattttaaaatagagacatttagtcctcatattttaatatctataattttag

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|26558732|gb|CA830967.1|CA830967

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

EST: gi|149083574|gb|EE172908.2|EE172908

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

EST: gi|87155515|gb|DY400304.1|DY400304

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

EST: gi|78111274|gb|DV529671.1|DV529671

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

EST: gi|22472877|gb|BU037357.1|BU037357

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

EST: gi|24766669|gb|CA401816.1|CA401816

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

EST: gi|93282383|gb|EB674647.1|EB674647

EST:     CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACT                         GTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA
genomic: CATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAA

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: 59

GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgtta ... tgtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAATGGTCCGTGGATAAAGTGCTTGAAGTCATCAATAAAACTTGCCGTTCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27