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

...tgtaaacttcaataatgatcatttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG

Basic information

species	Zea mays
transcript	GRMZM5G807639_T03
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 9

tgtaaacttcaataatgatcatttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatc---ttacgatt-tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG
|  || |||  ||   |  |   |       | |    |  |||    ||||  ||    |||| |  | | || |  || |   ||| ||   ||  ||  ||||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| ||||||||||||
tagaatcttgcatggcgtactactaattcttcctagaaaagctt----ggctagatatgcttttctgttttgtccccttaccctgttaagacaatacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 11

-tgtaaacttcaataatgatcat-ttggcatacc-attatg-atcctttgaaggctgtattaatttttttactctatctctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG
   |     |   |  |  | |  |   || |||  ||||| || || | ||   |  | || | | | | ||||  ||   |    | |  || |||||  ||||| |||||||||||||| |||||||||||||| ||||  |||||   ||||||||| ||||||||||| ||||||||| |||||||||| 
agatttttcttggtctttgtgagatcaacaaacctgttatgcattctctcaaa--ttcactattatgtattctctcccttattgctctgctcttaatgat--agGACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTCAAA

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G02530.2 (Glycine max), 3'ss of exon 11

--tgtaaacttcaataatgatcatttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatcttacgatttatgat-atagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG
  | |||    ||||  |     ||  |  | |  | |||  | | |  ||  || |||| | || | | ||| |  || |||    |   |  | || ||||||| |||||||||||||| |||||||||||||| ||||  |||||   ||||||||| ||||||||||| ||||||||| ||||||| || 
tgtttaattgccaattcttgatgttgtgtttcctgtcatgtccttatatag--tggattactattgtcattctcttcct-tattggtctgctcttaatgatagGACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6

-tgtaaacttcaataatgatcatttggcataccattatgatcctttgaagg--ctgtattaatttttttactctatct-ctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG
   | ||  |  ||    ||    || |  |   |||  || || | | |    | |  | |||||| |    | | | ||||  ||| |   ||||  |  |||||||||||||||||||||||||||||||||||||||| |||| |   |||||||||||| || ||  |  |||||||  | ||||| |||
tcatcaatatatattgaaattgcctgacgcatt-ttagcatgctatcaggcacttctggtgatttttgtctgttttttgctgtg-cttgctgcttat--tgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 12

tgtaaacttcaataatgat-catttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatcttacgattta------tgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG
       ||| || ||| |  || |     |   |     ||| ||  ||    ||||||||| || ||||  | | |   |  | |  | |       |  | |||||| || || |||||||| |||||||||||||||||||  ||| |    |||||||| || || ||||| || |||||| | ||| | || 
-------ttccatcatgctgtatataatccattttccctttccatttcagaaaatattaatttgttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA

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|67025111|gb|CO453860.1|CO453860

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|32935625|gb|CF040437.1|CF040437

EST:     ATTCTCAGAACACCTTTGCAATGCTGA-GTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ATTCTCAGAACACCTTTGCAATGCT-ATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|7031253|gb|AW461141.1|AW461141

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|60343714|gb|DN210687.1|DN210687

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|31349005|gb|CD433362.1|CD433362

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|6056485|gb|AW090875.1|AW090875

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAG-TGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|211169877|gb|FL077606.1|FL077606

EST:     GATTCTCAGAACACCTTTGCAATGCTATCTACRNKTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|6020821|gb|AW065749.1|AW065749

EST:     GATTCTCAG-ACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

EST: gi|67031724|gb|CO460473.1|CO460473

EST:     GATTCTCAGAACACCCTTGCAATGCTATCTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGGC-CAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 115

GTGCCGATGCCAAGGCTCAGGAAGCGTATTGCAAACCGTCTTAAGGATTCTCAGAACACCTTTGCAATGCTATCTACATTTAATGAAGTTGACATgtaagtgttc ... tatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 155

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gaaggctgtattaatttttttactctatctctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG

      tgtattaattttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaaacttcaataatgatcatttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatcttacgatttatgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG

- - - - - - - - - tcatttg
- - - - - - - - - - - - -gcatacc
- - - - - - - - - - - - - - - - - - tgatcct
- - - - - - - - - - - - - - - - - - - - - - - - -gctgtat