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

gtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

Basic information

species	Zea mays
transcript	GRMZM2G104373_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 4

gtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA
|||||| | |   |||     ||   ||| ||||  | ||       || | || || ||| ||| ||| |    |||||   | ||||||||||||||| || |||||| |||| |||||||| ||||||||||||||| | ||| | || ||||||||||| |||||||||||||| || || ||||
gtgcttttctacaatg-----tttcaagttctgtcttattgg-----aaacctgcttcgttcttatcaata----gtttttgggtgcagATACACACATCTAAGATGACATTGGCAGATGATGTTAACCTAGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTA

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 4

gtgcttctatgtgatgaaagcttctg--agtcctgttcttttaattaaaaagcatgatttgtt---------gttaccaaaattttgt--tttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA
   |    ||  ||||   | |||||    | || |    |   |||| | ||||  ||||||         | |   | | | |  |  ||||      |||||||||||||||  |||||| | ||||||||||| ||| | ||||| ||| ||||| | |||||||| || || || ||||| || ||||| || ||||
-acccaacataagatgtt-gtttctgctgattctatgtgatatcttaacatgcatactttgttcaatcatatgcttatacattctcatactttggaattaagATACACACATCGAGGATGACATTAGCTGATGATGTCAACTTGGAAGAATTTGTTATGACTAAAGATGAATTCTCTGGAGCTGATATAAAGGCAATATGTA

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 4

gtgcttctat--gtgatgaa-agcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA
|| |  | |   |||||    |  || |   || | || | | ||||    || | ||| || |        ||||   |    || |  ||||||||||||| || |||||  ||||||| ||||| ||| ||||||||||| | ||| ||||||| ||||| ||||| ||||| || ||||| || || |
gttccacaactggtgatccttaagttttctttctttttttgtgaattttctagaaagatctgatcggtttttaattgcatgcc-attattagATACACACATCAAAGATGACTTTGGCTGAAGATGTGAACTTAGAAGAGTTTGTAATGACAAAAGACGAGTTCTCAGGAGCTGATATAAAGGCAATATGCA

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4

-------gtgcttcta-tgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA
        |  ||||| || ||||  |  | |   | | |||||        |||     |  ||  |||          ||   |||    |  |||||||||||||||| ||||| ||  | || ||||||||||| ||||||||| | ||| | ||||| ||||| ||||| ||||| || ||||| || || |
gtaatatataattctactgagatggcaaat-caatgacttgttcg-------aaactttcttgttcattgaggttgtgggttctgtttataaaatagATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4

--------------------------gtgct-tctatgtgatgaaagcttctgagtcct---gttcttttaattaaaaagcatgatttg----ttgttaccaa---aattttgttttgatga---gcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA
                           |||  | |     ||     | || || | ||   |     | ||| |  || | ||  |||     | |||| ||   ||| |  |||   | |   ||||||||| ||||| |  |||||| ||||||||||||| ||| | ||||| ||| ||||| | || ||||||||||| || ||||| || ||||| || || |
gtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3

------gtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttg-ttgttaccaaaattttgttttgatga-----gcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA
       |   | |||||| ||| |  ||     |   ||| | || || ||  |   |  |||| | | |        ||| |||| ||||     |||||| || || || | ||||||  |||||||||||||||||||||| |||||| | ||| | |||||||||||||| ||||||||||| || || || ||||
tcttcattagctttatgtg-tgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA

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|149110574|gb|EE294195.2|EE294195

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGGGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|37401158|gb|CF637942.1|CF637942

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|60394503|gb|DN227373.1|DN227373

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|87156235|gb|DY401024.1|DY401024

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|71318153|gb|DR795840.1|DR795840

EST:     AGATTGAATTCCCTTTTCCTGATGTCAAGACTAGGCGGCGCATTTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|40302995|gb|CK347382.1|CK347382

EST:     CAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: CAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|60399673|gb|DN232483.1|DN232483

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|6828042|gb|AW331685.1|AW331685

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|74232019|gb|DT639933.1|DT639933

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|5895801|gb|AW037047.1|AW037047

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|4887302|gb|AI677401.1|AI677401

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|47961685|gb|CN844394.1|CN844394

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|21987487|gb|BQ779015.1|BQ779015

EST:     AGATTGAATTCCCTTTCCCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACAGTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|60357188|gb|DN224161.1|DN224161

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|20301592|gb|BQ164535.1|BQ164535

EST:     AGATTGAATTCCCTTAACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|74232018|gb|DT639932.1|DT639932

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGGGCATTTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|78103532|gb|DV521960.1|DV521960

EST:     TGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: TGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|211268017|gb|FL355150.1|FL355150

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|76917636|gb|DV166930.1|DV166930

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|78023275|gb|DV491662.1|DV491662

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|5650117|gb|AI920477.1|AI920477

EST:     CGGCGCTTCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: CGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|32847761|gb|CD987442.1|CD987442

EST:     AGATTGAATTCCCTTTACCCGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|78544201|gb|DV621699.1|DV621699

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|67015613|gb|CO444362.1|CO444362

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

EST: gi|6022662|gb|AW067474.1|AW067474

EST:     AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAG                         ATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT
genomic: AGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTT

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), 48 (downstream exon)
Score: 215

TATTGAAAGTCTTGATCCAGCCTTGCTTCGCCCAGGTCGAATTGACAGAAAGATTGAATTCCCTTTACCTGATGTCAAGACTAGGCGGCGCATCTTCCAGgtgcttctat ... tgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 359

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 328

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

                                     ttttgtttt  CT-rich tract
                                 aaaattttgttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttgttgttaccaaaattttgttttgatgagcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG