ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgtgtttccttggctgcatagtggcaaatgcgcttttttgtcctgcatagtaaattgaatttgttggtataatttgaattgacag

Basic information

species	Zea mays
transcript	GRMZM2G152526_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152526_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g23120.1 (Oryza sativa), 5'ss of exon 4

GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtat---atttgtgt-ttccttggctgcatagtggcaaatgcgcttttttgtcctgcatagtaaattgaatttgttggtataatttgaattgacag
||||||||||||||||| || || ||||| ||||| ||  | |||||||||||||||||||| || ||||||||||||||||| || ||| | |||||||||||   || | | | ||  ||| ||    |  | | |   |   || || |  |  | |||| | ||||  ||||| |   ||   | |||||||
GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTCAAGACGAAGAAAATATTTGTTGGTGGATTACCATCTGCTTTGAAAGAAGgtattacatgtatatattgtttgcctaaccatggactagctcatattattattttata-agtatactgaacatgttgatgcgat--aatttgacag

upper sequence: GRMZM2G152526_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0117g00150.t01 (Vitis vinifera), 5'ss of exon 4

GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatt---------tgtgtttccttggctgcatagtggcaaatgcgcttttt-tgtcctgcatagtaaattgaatttgttggtataatttgaattgacag----------------------------------------------------------------------
||||| ||||| ||||| || || || ||  ||| ||  | ||| |||||||| || |||||||| ||||||||||||||||| ||  |  | |  ||||||||| |           || ||  |       | | |    |||||  |  || | | |||   |  ||| | |||| | |  | | | | |  || || |                                                                      
GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAGgtataatatataatgtcatgcttgatctatcaaaaaatatataatgccatgcttgtattctgatgaaaaaacttaattggcttatgttaatagc-ttaactgtctcatttacttaaaatttttctttttcctccctctctctctctcaactctggcctgttcaaataatcag

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|6020836|gb|AW065764.1|AW065764

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|19770245|gb|BQ034966.1|BQ034966

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|22546340|gb|BU098651.1|BU098651

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|24763190|gb|CA398373.1|CA398373

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|22472797|gb|BU037277.1|BU037277

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCC
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCC

EST: gi|211034280|gb|FL145437.1|FL145437

EST:     CAAGACGAAGAAAATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTT
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTT

EST: gi|211043651|gb|FK991975.1|FK991975

EST:     CAAGACGAAGAATATTTTTGTTGGGGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|22472280|gb|BU036760.1|BU036760

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|21760066|gb|BQ635607.1|BQ635607

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|22546609|gb|BU098920.1|BU098920

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|14569276|gb|BI097599.1|BI097599

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|22715554|gb|BU197829.1|BU197829

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|19770110|gb|BQ034831.1|BQ034831

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

EST: gi|211034279|gb|FL145436.1|FL145436

EST:     CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG                         ATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA
genomic: CAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAA

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: 407

GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgt ... gaattgacagATGAATTCAAGGAATTCTTTTCCAAGTTTGGGAAGGTTGTGGAGCATGAAATCATCCGTGACCATGCAACCAACCGGTCACGTGGATTTGGTTTTATAGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 233

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAGgtatatttgtgtttccttggctgcatagtggcaaatgcgcttttttgtcctgcatagtaaattgaatttgttggtataatttgaattgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG