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

...tttcttcaaaaagaaaaaaatgtttgctttctgatgatttgtttatgttatttattcatctattattttacaagcaaccctaattcttaactgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG

Basic information

species	Zea mays
transcript	GRMZM2G169462_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 5

tttcttcaaaaagaaaaaaatgtttgctttctgatgatttgtttatgttatttattcatctattattttaca------agcaaccctaat-tcttaactgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG
       ||||    |  | || || |  | |  |  | | ||| | ||||  ||   | | ||| ||||        || ||||||||| | || |||  || ||||| |||||||| ||||| |||||||||||||||||||| ||||| |||||||||||  || |||||||||||||||||||||| || ||||| ||||
------gaaaattggatcactgattacagtttattcttctctttgt-ttatccatatctgttttactttatgtttcagagaaaccctaatattttgacttctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 5

tttcttcaaaaagaaaaaaatgtttgctttctgatgatttgtttatgttatttattcatc----tattattttaca----agcaaccctaat-tcttaactgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG
        || | ||  | ||   |||||   | |  ||  || |  ||||||||||||     | ||| ||||      ||  |||||||| | || |||| || ||||| |||||||| ||||| |||||||||||||| ||||| ||||| |||||||||||  || |||| ||||||||||||||||| || ||||||||||
--------aagaaaattagatcactgcttatagtttgttc-ttcactttatttattcatatttgttttactttatgtttcagagaccctaatattttgactgctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGTATTCTGGTTTTCCATGATTCACGTGTCCGGGACTTGATGAACATGAAGATATTTGTTGATACAG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 5

-tttcttcaaaaagaaaaaaatgtttgctttc-tgatgatttgtttatgttatttattcatctattattttacaagcaaccctaattcttaactgttgc-cagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG
  |  |||     |      || |    |    ||   |||| | |    ||    |||| ||||    || |     |   |  || | | |||||   ||||| || ||  |||||||||||||||||||||| || || |||||||||||| ||||  |  | |  |||||||| |||||||| || ||||| ||||
catgtttcttcttgcgttttatctccattagagtggaaatttatatggaatacaatttcagctata--cttcccttttatgttggtt-taatctgttttgcagGTAAACCCAGCGGATGTTATTATTTTGGAAGGTATCCTTGTTTTTCATGATCCACGAGTGCGAGCATTGATGAATATGAAGATATTTGTTGACACAG

upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 5

--tttcttcaaaaagaaaaaaatgtttgctttctgatgatttgtttatgttatttattcatctattattttacaagcaaccctaattcttaactgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG
    |  ||   ||       |  ||   |||| | |  ||  ||| ||||      | |   ||   || | || |  |  |  |    ||   ||| ||||| || ||||| ||||| || ||||||||||| || ||  |||||||||||   ||  || |||| ||||||||||||||||| || ||||||||||
agggtggtcctgaatcctgtgagattatatttcaggtacttgatttctgttcccgggttac--atgcattgagaaccctcattgctatgaaatatttggcagGTCAACCCTTCAGATGTGATAATTTTGGAAGGCATACTCATTTTTCATGATCTTCGTGTCCGGGAATTGATGAACATGAAGATATTTGTTGATACAG

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|78107197|gb|DV525615.1|DV525615

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|211396287|gb|FK980044.1|FK980044

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|4609834|gb|AI600673.1|AI600673

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|211393676|gb|FK980040.1|FK980040

EST:     TCCCTAACTACAACTTCA-GACATACAAAAGTGTCC-AAATGCCAGGAAG                         GTTAATCCCTTCGGATGTAAT-ATTTTTGGAAGGAAT-CTAGTTTTTCATG
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCC-TTCGGATGTTATTATTTT-GGAAGGAATTCTAGTTTTTCATG

EST: gi|71439100|gb|DR820150.1|DR820150

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|148987214|gb|EE031046.2|EE031046

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|211396292|gb|FK980049.1|FK980049

EST:     CCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAAGGAAG                         GGTA-TCCTTCGGATGTTATTATTTTGGAAAGAATTCTAGTTTTTCATGA
genomic: CCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAA-GGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGA

EST: gi|5847365|gb|AW000444.1|AW000444

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|211396289|gb|FK980046.1|FK980046

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

EST: gi|211396288|gb|FK980045.1|FK980045

EST:     TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAG                         GNTANTCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: TCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT

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: 42 (upstream exon), 49 (downstream exon)
Score: 41

GCTACTTCTCTCTTGTATGCAAAACTTGAAATGTGGCAAAGCTGTTGACATCCCTAACTACAACTTCAAGACATACAAAAGTGTCCCAAATGCAAGGAAGgtaatatttt ... ctgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgttatttattcatctattattttacaagcaaccctaattcttaactgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG

                                       tcttaac  putative branch site (score: 112)
     tttattcatctattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttcaaaaagaaaaaaatgtttgctttctgatgatttgtttatgttatttattcatctattattttacaagcaaccctaattcttaactgttgccagGTTAATCCTTCGGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATTTTCGTTGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA