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

...tttcttctattttccctacttttctattaatgagaatgccaatatatttgtctcttaatgtcagtggactcagtgctgctatttttttcatataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATCTCGTGCAGCTTCGGAGATGGCTGATCTGCTGTACCACGCTATGGTGCTG

Basic information

species	Zea mays
transcript	GRMZM2G082214_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G082214_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16940.1 (Oryza sativa), 3'ss of exon 4

---------------tttcttctattttccctacttttctattaatgagaatgccaatatatttgtctcttaatgtcagtggactcagtgctgctatttttttcatataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATCTCGTGCAGCTTCGGAGATGGCTGATCTGCTGTACCACGCTATGGTGCTG
               | | |    |||||||||    ||| | |||| ||||||| ||||||||| |     ||       || |  ||          |||||||||  ||||| ||||||||||| |||||||  ||||| |||||||||||||||||| |    ||  ||      ||||||| |||| |||| |||||||| |||||||||
ttatattgccgtcgttctttcgccttttccctatccctctctcaatgtgaatgcccatatatttgac-----atacatactgatttggt----------ttttcatattttccagCGAAGAAGCTGGAGAGCTAAACCAAACACTGCTTGAGAACGAGGACGAGAGCCGCACAATCAGTGAGATGGGTGATTTGCTATACCACGCGATGGTGCTG

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|18163681|gb|BM333520.1|BM333520

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|32849363|gb|CD989044.1|CD989044

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|67018853|gb|CO447602.1|CO447602

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|78027709|gb|DV496096.1|DV496096

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|5108141|gb|AI739854.1|AI739854

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|148987058|gb|EE030883.2|EE030883

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCNAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|5686871|gb|AI939785.1|AI939785

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCCAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|33093406|gb|CF053400.1|CF053400

EST:     CGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAGGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: CGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|61118955|gb|DN559916.1|DN559916

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACTCTGCTTGAGAACGAGGACCCATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

EST: gi|211366681|gb|FK959526.1|FK959526

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTG
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTG

EST: gi|60349630|gb|DN216603.1|DN216603

EST:     TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACG                         TGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC
genomic: TGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATC

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: 92

TTAGTAGACGCCACGAGGAGAAAGTTACTGATGGAGGTGGCAAGCCATCATGGACGAAAAAGCTACTCCTTGATAACCAGCTACTTTGCTCGAAAATACGgtatatgatg ... tataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATCTCGTGCAGCTTCGGAGATGGCTGATCTGCTGTACCACGCTATGGTGCTG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 158

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 103

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 93

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atttgtctcttaatgtcagtggactcagtgctgctatttttttcatataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATCTCGTGCAGCTTCGGAGATGGCTGATCTGCTGTACCACGCTATGGTGCTG

       tcttaat  putative branch site (score: 93)
                                    tttttttcat  putative PPT
                                  tatttttttcatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttctattttccctacttttctattaatgagaatgccaatatatttgtctcttaatgtcagtggactcagtgctgctatttttttcatataatccagTGAAGAAGCTGGTGAGCTAATTCAAACGCTGCTTGAGAACGAGGACCAATCTCGTGCAGCTTCGGAGATGGCTGATCTGCTGTACCACGCTATGGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - -gaatgcc