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

...tacctctcaacctattgacctccccatctttgcaaaaaaaaaaaaaggtgctccgtttgaactgccctgctggttcttaatcttggtttcttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCATCATGTAATCTATGTGCGTTGCAATGTACAGCATTATTGAATTGAGCAG

Basic information

species	Zea mays
transcript	GRMZM2G022859_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G022859_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 4

tacctctcaacctattgacctccccatctttgcaaaaaaaaaaaaaggtgctccgtttgaactgccctgctggttcttaatcttggt----ttcttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCATCATGTAATCTATGTGCGTTGCAATGTACAGCATTATTGAATTGAGCAG
    |  ||   |||   |  |   | |    |||  |       |  ||||    |  |  |||      |||||| || || | |    ||  | ||||||||||||||||| ||||||||||| ||||||||| | || ||||| |||||||||||||||   ||| |  ||||||||||||| |||||| ||||||| ||
----ttacagtttataatcagcataagcgaaacaatgaggttgctacttgctagactgaagttgcatgttgggttctgaacctagttgctgtttctttctgcagGCAATGAAGATCAAAGAGTAGAACAGAAAGGGCTATCGCTTAGGTGTGTCATCATGTAAGAGATGCGAATTGCAATGTACAGTATTATTAAATTGAGTAG

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|71423683|gb|DR806127.1|DR806127

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|14243209|gb|BG840922.2|BG840922

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|60345888|gb|DN212861.1|DN212861

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|88754530|gb|DY538671.1|DY538671

EST:     AAGGGAGAGGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGGGTGTTTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|6653930|gb|AW267335.1|AW267335

EST:     AAGGGAGATGTCAACTCCNCAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|211292709|gb|FL181553.1|FL181553

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|211292700|gb|FL181544.1|FL181544

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAAGGGTG
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTG

EST: gi|60337925|gb|DN204898.1|DN204898

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|71423686|gb|DR806128.1|DR806128

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|31909793|gb|CD651096.1|CD651096

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|13389071|gb|BG462542.1|BG462542

EST:     AAGGGAGATGTCAACTCCACAGAATAACAAAAAGAACCANCCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|76016546|gb|DT943716.1|DT943716

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|32165108|gb|CD670426.1|CD670426

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|78025429|gb|DV493816.1|DV493816

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|16379365|gb|BI992896.1|BI992896

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGAATGAACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|76913969|gb|DV165351.1|DV165351

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|211343001|gb|FL470860.1|FL470860

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|60350937|gb|DN217910.1|DN217910

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|14242746|gb|BG840531.2|BG840531

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|211241891|gb|FL451480.1|FL451480

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|60351107|gb|DN218080.1|DN218080

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

EST: gi|60350383|gb|DN217356.1|DN217356

EST:     AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAG                         GCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA
genomic: AAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCA

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: 186

GGAAAGTGGGAAAGGGAACATACGATGGAGGACATTCTGACCAGCTTAAAAAGGGAGATGTCAACTCCACAGAATCGCAGGCTGTACCAACCTCATGAAGgtattttttt ... ttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCATCATGTAATCTATGTGCGTTGCAATGTACAGCATTATTGAATTGAGCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 206

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aggtgctccgtttgaactgccctgctggttcttaatcttggtttcttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCATCATGTAATCTATGTGCGTTGCAATGTACAGCATTATTGAATTGAGCAG

                             tcttaat  putative branch site (score: 166)
                                   tcttggtttcttctct  CT-rich tract
                            ttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctctcaacctattgacctccccatctttgcaaaaaaaaaaaaaggtgctccgtttgaactgccctgctggttcttaatcttggtttcttctctgcagGCAATGAAGACCAAAGAGTAGAGCAGAAAGGGGTGTCTCTTAGATGTGTCATCATGTAATCTATGTGCGTTGCAATGTACAGCATTATTGAATTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG