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

...gttttagctgtgctgccatcttccatttcaaatggttagattggctattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC

Basic information

species	Zea mays
transcript	GRMZM2G145376_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1

gttttagctgtgctgccatcttccatttcaaatggttagattggctat--tcaaaatcatctctgacatgcctttaattatttcaat-ttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
  ||||  | |  |   | ||     |        ||  ||| | |||  |   | |  | | |   || |  ||  | |||   || ||| || |||||||||| || ||||||||||| || || |||||||| || || |||||||||||    ||||| ||||| | ||||||||||||  |||| || ||| |  |||
-attta--tttattattagctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC

upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G32750.1 (Glycine max), 3'ss of exon 1

------------------------------------------------------------------gttttagctgtgctgccatc--ttccatttcaaatggttagattggctattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
                                                                   | |    |   ||||   |  ||   |||  | || ||   |||   |||  | |  |     || |   | || ||  | | |  ||  || |||||||||| || ||||||||||| || || |||||||| || || |||||||||||    ||||||||||| | ||||||||||||  |||| || ||| |  |||
gtattctttattttttagctggtgtttggtgcttttttgttcgtgatgactctatttctatttgatttctgtattaaactgctggcaattttgttttgagtgattctgttgttgatttgatactaaactagaaa--gcgttgat--tctgatattgaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCGCATCAGTTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC

upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G57890.2 (Arabidopsis thaliana), 3'ss of exon 2

gttttagctgtgctgccatcttccatttcaaatggttagattggctattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
        | | ||  | | |  |||  ||   |||   |    || |     | |       |  ||   || ||   | |  || ||  ||| ||||||||||||||||||||||||| || |||||||| || || || ||||| |||  |||||||||||| | ||||||||| ||| | || || ||  || |||
-------gtattctatcgtttctcatcacatg-ggtcgaaccaactttattggagc----taaaattgttatttatatctccttttcatcatttctgcagCTTGTTCGCAGCAACAGCCGTCGATTTATGCCATCACAGGCAGATGATGAAGCTCATCAGTTGTCATATCTGCAAAAACATTTAGCAAACATCATTTCTC

upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G42230.1 (Arabidopsis thaliana), 3'ss of exon 1

gttttagctgtg-ctgccatctt--ccatttcaaatggttagattggctattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
 ||||| |  |   ||   || |  |  |||| |     | | | |     ||    |      |||  |    ||||  |||||  || ||   | |||||||||||||| ||||||||||| || |||||||| || |   | |||||||||  |||||| || || | |||||||||||| || || |||||| || |||
attttaccgataattgttctcattactgtttctatcatatgggtagagacatccttgtagctgttgagtttaagttaa--atttcctttcat-catcttgcagCTTGTTCGTAGCAACAGCCGTCGGTTTATGCCATCACCGACAGATGAAGAAGCTCATCAATTATCGTATCTGCAAAAGCACATTGCAAATATTATTTCTC

upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G57890.1 (Arabidopsis thaliana), 3'ss of exon 1

-----gttttagctgtgctgccatcttccatttcaaatggttagattggctattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
      | || | | | ||  | | |  |||  ||   |||   |    || |     | |       |  ||   || ||   | |  || ||  ||| ||||||||||||||||||||||||| || |||||||| || || || ||||| |||  |||||||||||| | ||||||||| ||| | || || ||  || |||
cactgttctttggtattctatcgtttctcatcacatg-ggtcgaaccaactttattggagc----taaaattgttatttatatctccttttcatcatttctgcagCTTGTTCGCAGCAACAGCCGTCGATTTATGCCATCACAGGCAGATGATGAAGCTCATCAGTTGTCATATCTGCAAAAACATTTAGCAAACATCATTTCTC

upper sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1

gttttagctgtgctgccatcttccatttcaaatggttagattggctattcaaaat-catctctgacatgcctttaa--ttatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC
    || |  | |||   ||||   | |  | | | ||  |    | || |   |   |     |  ||   |||   |||| ||  ||        ||||||||||| ||||||||||||||  | ||||||||||| ||||| ||||||||   |||||| || |||| | | ||||||||  |||| || || ||| | |
---ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC

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|211288680|gb|FL312631.1|FL312631

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|148945185|gb|EC890388.2|EC890388

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211208734|gb|FL358266.1|FL358266

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|149071042|gb|EE159445.2|EE159445

EST:     GCCCACCTCCCGCGT-CGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAGGCTGATGAAGAA
genomic: GTCCACCTCC-GCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211012394|gb|FL319255.1|FL319255

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|78079827|gb|DV508239.1|DV508239

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211347336|gb|FL342021.1|FL342021

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCTTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211392160|gb|FL368046.1|FL368046

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211260626|gb|FL351803.1|FL351803

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211089442|gb|FL362867.1|FL362867

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGATGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|148935831|gb|EC879879.2|EC879879

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211158616|gb|FL316326.1|FL316326

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGAT
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGAT

EST: gi|211303808|gb|FL321303.1|FL321303

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|76934101|gb|DV173728.1|DV173728

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|89762105|gb|DY689855.1|DY689855

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|148946192|gb|EC891487.2|EC891487

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211424273|gb|FL309087.1|FL309087

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|149011570|gb|EE042404.2|EE042404

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211316366|gb|FL341233.1|FL341233

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|148978503|gb|EE026182.2|EE026182

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211263174|gb|FL356041.1|FL356041

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

EST: gi|211390755|gb|FL310442.1|FL310442

EST:     CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAG                         CTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA
genomic: CGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAA

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: 44 (upstream exon), 39 (downstream exon)
Score: 30

CGTTCCGCGGAGCGCGCACAAGGACTCGCCCGCCGTGGCGGACGTCTGGCCGTCCACCTCCGCGTTCGATGGGTACCTCTCCGCGCTCTCCCCGATCCAGgtcaggatta ... ttttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 37

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 50

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC

                                           tatttttt  CT-rich tract
                    atgcctttaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttagctgtgctgccatcttccatttcaaatggttagattggctattcaaaatcatctctgacatgcctttaattatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC

- - - - -gtgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgcc