ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...gcattcaaacatcaagtgaggggaaccaagcaccctctaaaaactacaatgtgaattgtagttatgcttctaatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTTTCACGTTTGAG

Basic information

species	Zea mays
transcript	GRMZM2G097726_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 4

gcattcaaacatcaagtgaggggaaccaagcaccctctaaaaactacaatgtgaatt--gtagttatgcttc-taatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTT----TCACGTTTGAG--
  || |||    || |        |   ||  |  | | ||      |||    |||  |   || ||      ||   | | | ||  ||| ||||||||||| ||||||||||||||| ||| ||||||||  |||   | |||| | || | || ||  |  |  || |||||||||||||| || |||    | | | |      
--atccaaggtacatgcact----atttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagcagGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCA-TTGACGAGAT--ACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATTTAT

upper sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g08880.3 (Oryza sativa), 3'ss of exon 4

gcattcaaacatcaagtgaggggaaccaagcaccctctaaaaactacaatgtgaatt--gtagttatgcttc-taatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTT----TCACGTTTGAG
     ||  ||        |    |   ||  |  | | ||      |||    |||  |   || ||      ||   | | | ||  ||| ||||||||||| ||||||||||||||| ||| ||||||||  |||   | |||| | || | || ||  |  |  || |||||||||||||| || |||    | | | |    
---cccatccaaggtacatgcactatttagttcttttttaatttggtaatcaccattctgcgattctgaaagacaaacatttcatttggactaatctcttcagCAGGTGGAGTCAAAAAGACGGAGAAGGTGACTGCCCCCCAGATTCA-TTGACGAGAT--ACACCTGGATGTACAAAGCCTTCTCAAGTTGGTGTAATGCTATT-

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|211224876|gb|FL455272.1|FL455272

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|148940632|gb|EC885443.2|EC885443

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|78180631|gb|DV550959.1|DV550959

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|67017898|gb|CO446647.1|CO446647

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|148942300|gb|EC887317.2|EC887317

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGCCAAAAAGGCGGCGAAAGTGATGGCCGTGCTGATT
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATT

EST: gi|148941206|gb|EC886093.2|EC886093

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|78074294|gb|DV502728.1|DV502728

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|93282376|gb|EB674640.1|EB674640

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|4967167|gb|AI691875.1|AI691875

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CTGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|8551650|gb|BE128821.1|BE128821

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|28909803|gb|CB331108.1|CB331108

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|91872374|gb|EB402331.1|EB402331

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|32825292|gb|CD965014.1|CD965014

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTA

EST: gi|78082597|gb|DV511009.1|DV511009

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAA-GGCGGCGAAGGTGATGGCCGTGCTGA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGA

EST: gi|211072814|gb|FL228291.1|FL228291

EST:     AAGATGGGTGAGAATTCACCTGAAAGCTACGGCGCAATCAGAAGAAAAAG                         CCGGGGGAGTCAAAAAGG
genomic: AAGATGGTTGAGAATTCACATGAA-GCTACAGCGCAATCAGAAGAAAA-Ggtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGG

EST: gi|78074295|gb|DV502729.1|DV502729

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|76927199|gb|DV171172.1|DV171172

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAAGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|67022285|gb|CO451034.1|CO451034

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|50336946|gb|CO532072.1|CO532072

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|91872230|gb|EB402187.1|EB402187

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|22818819|gb|BU498909.1|BU498909

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CTGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|60399583|gb|DN232394.1|DN232394

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|148951992|gb|EC897774.2|EC897774

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|9733234|gb|BE511986.1|BE511986

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CTGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|32823010|gb|CD962719.1|CD962719

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCT
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCT

EST: gi|60354816|gb|DN221789.1|DN221789

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

EST: gi|60357704|gb|DN224677.1|DN224677

EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA

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: 393

AGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTTTCACGTTTGAG

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 152

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 105

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acaatgtgaattgtagttatgcttctaatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTTTCACGTTTGAG

                                              tctcttc  CT-rich tract
                         taatagtataacttta  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattcaaacatcaagtgaggggaaccaagcaccctctaaaaactacaatgtgaattgtagttatgcttctaatagtataactttaactgatctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTATGAAATCTATGCTCGGTTGTACAAAGCCTTCCCACGTTTCACGTTTGAG

gcattca
- - - -aacatca
- - - - - - - - - - - - - caagcac
- - - - - - - - - - - - - - - - - - - - -aactaca
- - - - - - - - - - - - - - - - - - - - - - - - - -tgaattg