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

...ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

Basic information

species	Zea mays
transcript	GRMZM2G121942_T03
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 3'ss of exon 2

-ttaaa-ggttcaactggatcttag-tcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaattta-ctatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
 |||    ||| || |   |  ||  | |||| ||  | ||  |||      |  | |   ||||| |     ||  || ||  | || | | ||  || |||||||||||| |||||||||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||  | ||||
tttattcagtttaaatatgttgtaccttttcaatgaac-tttggtaat---atccttttgtattttgaccatgatgttgatatgataaatcatcttctttaaagGCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G40200.2 (Glycine max), 3'ss of exon 1

----------------------------------------------------------------------ttaaaggttcaactggatctt--agtcttcagtgt-tcgttcagtagct-----------aggttttctgacattttcaa-tgcaatactgctaacacaatttac---tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                                                                      || | | | | | |  || ||  | | |||||| | ||  || ||  |              |||   |    ||||||| | |  | | |  ||   | |||     | ||  | |||| || |||||||| ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
gtagagattctattcccaatttccttgaaacgctctttccctctttccgttcactcgctccgttatgaagttcaggctgcgattcaattttgtacttttcagtttctcaatctgtgacctatgtgaattggagttaattagggttttcaaattcggtcccg--aattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1

---------------------------------------------------------------------------------------ttaaaggttcaactggatcttagtct-tcagtgttcgttcagt---agctag-gttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---agGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                                                                                        || |  |||   |   | | ||| | ||| | |  |  |  |   | || | |||   |    |||| ||      |     ||   |||||   | ||  |   ||||||| |||||||| ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   |||||
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttct-ttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1

ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttac---tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
        |   | |  ||| | |||      |  ||  | | |  || |  |  |   |||  ||| |  | | |  ||   | |||     | ||  | |||| || |||||||| ||||| || || |||||||||||||| ||||||||||||||||| || || ||||| ||||||   |||||
----gtacttttcagtttctcaatctgtgacctatgtgaattgg--agttaattagggttttcaaattcggtcccg--aattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1

---------------------------------------------------------------------------ttaa---aggttcaactggatcttag------tcttcagt-gttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---agGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
                                                                           ||||   | |   | ||| |   | |      | | |  | |||| |  |   | ||||||||    ||      |   | |  ||  | | || |||  | |||      |||| || |||||||| |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| ||||||   |||||
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagc----agatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 3'ss of exon 1

ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaata-ctgctaacacaa--tttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
    ||||  |  ||  |||||   |  ||  |   |  |  |  | ||           ||| |||  || | ||  |         |||  | |||   |||| || |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| || || ||||||||||||  ||||||
aattaggtcgatttgtttctta---taaagcatatatagatgaaatcgggaacaatttgctttaaatttaacatcttttggtttgggtttttttcttttgcagGCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1

ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagc--taggttttctgacattttcaat-gcaat--actgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
      ||         | ||  | ||     | | || | | |    | |   |    ||| || | | | |||  |     |     || |   |||  | |||| || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||
-----tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT

upper sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ07968 (Selaginella moellendorffii), 3'ss of exon 1

ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT--------------
                          | |||   || ||  |  ||     |||  |  |  |||  |    | || || |   ||||  |       |||| |||||| | |||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || ||  |   | ||||              
-------------------------gtaagtaagcgctcgatctct----cttcccatttcctcagcg----attggtagcg--atttcttgc-----agGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA

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|211191930|gb|FL276018.1|FL276018

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211194324|gb|FL276026.1|FL276026

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211191923|gb|FL276011.1|FL276011

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211191934|gb|FL276022.1|FL276022

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         -C--G--ATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211194323|gb|FL276025.1|FL276025

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211191922|gb|FL276010.1|FL276010

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211359713|gb|FL342921.1|FL342921

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCTGA-CAAAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211194325|gb|FL276027.1|FL276027

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211088952|gb|FL225885.1|FL225885

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211191933|gb|FL276021.1|FL276021

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTT-CAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAA

EST: gi|211191925|gb|FL276013.1|FL276013

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211191928|gb|FL276016.1|FL276016

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|37387079|gb|CF630732.1|CF630732

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211191926|gb|FL276014.1|FL276014

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

EST: gi|211194322|gb|FL276024.1|FL276024

EST:     AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAG                         GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA
genomic: AGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAA

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: 602

ATCTTCTTCACTGGGTCCTCCGCTGCTTCTAGTCACGCATCTAAATCCGGAGTTGCCAGCATTCGCTTGAGGTGCCGGACCACAGCACACCATCATGCAGgtgggtagta ... tatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 577

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 475

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

                             tgctaac  putative branch site (score: 475)
                                      aatttactatttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT