ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgatgctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatcttctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA

Basic information

species	Zea mays
transcript	GRMZM2G139880_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 10

------------gtgagccaa--ccatttttacgaaaaatatgaaatctgcatatatgaacttgatgctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatcttctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA
             | |   ||    ||||     ||||  ||| ||  | || |||||||   |      ||| ||||| |  ||  |     |   | |   || | |       || | ||  |||   | | || ||||    |  ||||||||| |||||||||| || |||| ||| |||||||||||||||||| |||| ||||||||||||||||| || |||||||||||||||||| | || |||||||
gtaagcaactcaataatttaaatttatttcattcaaaagcatggaacattcagatatgaaacagcactcctga-gttttgtgatgattcaccttacttatcaatggtga-------tgtctataaatccgtttaattatatg--aatactatgtgcagGTTTTGAAGATTAACCCTTTGAAGAAGGATATAGATTCTTTCGTGGCATCAGACTTCAAGCTGGTCGGTTATGATCCTCACCAGAAGATTGAAATGAAAA

upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9

gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgatgctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatct-tctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA
                                      ||| || |    ||| ||| | | |||| ||||  |    ||   ||        ||  | |  |    |||| |   | ||| |||  |       || | |  |||||||||||||||| ||   ||| || ||||||||||||||  |||| || || ||||||||  | || |||| ||||||||||||| |||| ||||| |
-------------------------------------gtatgtgta---aatgttttaaggattttatttgctttaacgtagatgcccacagatatataccat---tatgcgttcgtataaattgcctaaa---tttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA

upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10

gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgat--gctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatcttctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA
                        || || ||      | || | | ||  |  ||||| ||||   |  |      | | |     | ||  ||    |    ||||  | |  ||| |   ||   |      ||| | | ||||||||||||||||| ||   ||| || ||||||||||||||  ||||  | || ||||||||  | || |||||||||||||||||| |||| ||||| |
----------------------gtatgtgtaa---atgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttc--cttgttgattacctaaa---cttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA

upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA06G01280.3 (Glycine max), 3'ss of exon 10

gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgatgctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatcttctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA
                                                       |   |||  | ||| |    | | |  || | | | || ||| | | | |   |  | |  ||||  ||||       |||   |||||| |||||||||||||||   ||| || ||||||||||||||  ||||  | || ||||||||  | ||||||||||||||||||||| | || |||||  
------------------------------------------------------gtatgtgtaatgtttagcacttctttaagtttatcttttgactcttt-tacttgtttaccccctaa--tgta-------cttcattgcagACTTTGAAGATAAATCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC

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|84980638|gb|DW530987.1|DW530987

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

EST: gi|211061450|gb|FL335153.1|FL335153

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTAAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

EST: gi|60397930|gb|DN230746.1|DN230746

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

EST: gi|78022008|gb|DV490395.1|DV490395

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

EST: gi|60341313|gb|DN208286.1|DN208286

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

EST: gi|6827015|gb|AW330658.1|AW330658

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCTTGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

EST: gi|148983313|gb|EE029285.2|EE029285

EST:     ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCA                         ATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA
genomic: ACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCA

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: 45 (upstream exon), 49 (downstream exon)
Score: 170

TCCAGGAGATTTTGTCCATGTTATAGGGGATGCTCATGTCTATAGAAATCACGTTCGAGCTCTGGAGGAACAGATTCAGAAGATGCCTAAACCATTTCCAgtgagccaac ... ttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 98

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 80

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgatgctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatcttctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG