ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagtaaaagtgtctttttatctgacttctaaaggaatgaacagtgttagcatatgtgagttggggcctgtttctgtagatagatttatgttataa...

Basic information

species	Zea mays
transcript	GRMZM5G800734_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G800734_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g33810.5 (Oryza sativa), 5'ss of exon 4

TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgag---taaaagtgtcttttt-atctgacttctaaaggaatgaacagtgttagcatatgtgagttggggcctgtttctgtagatagatttat--gttataa
|   ||||||    | |||||||||||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||||| |||||||| ||||  ||||||||||      | | |  || |   |  ||||||||    |  |  ||  || |  |  |  |||  ||   | |||    |||  ||    |||  ||  | |
TACTTCCACTACATTGTCTGGACCTGAAGAAACTGAAGAGGATGGTGGAGATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagttcgataataactataggacgtgacttct----gtttttactttgct--ctgagttgatctgaaacttgtgctggtatctatccgtattagtcttca

upper sequence: GRMZM5G800734_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G12950.1 (Glycine max), 5'ss of exon 6

---TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagtaaaagtgtctttttatctg-acttctaaaggaatgaacagtgttagcatatgtgagttggggcctgtttctgtagatagatttatgttataa
   ||  ||  |||     |||||  | || |||||    || ||    ||  |||| ||||| || ||||||||||| ||||| |||||||||||||  |||||      ||  | | | ||| ||  || |  |       |||   |    ||     | |  |    |    |   | | |   |  |    ||   |  
AGGTGCCTCTGCTGAAAATTCTGGGGCAGATGAGAC---AGAAGATTTGGGAAATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatatagcactatttttctacatgcatatgctcttaaatcttctccctttttgaaagaaatcatgaattttactttatgattgaagacttgaagtt-

upper sequence: GRMZM5G800734_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 6

---TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagtaaaagtgtctttttatctgacttctaaaggaatgaacagt-gttagcatatgtgagttg-gggcctgtttctgtagatagatttatgttataa
   ||  ||  |||     |||||  | || ||||| || ||    |||    |||| ||||| || ||||||||||| ||||| |||||||||||||  |||||      ||  | | | ||| ||  || | | |     |||      | |||     |    | |   | |  |   ||| |      |    ||  |   
AGGTGCCTCTGCTGAAAATTCTGGGGCAGATGAGACCGAAGATTTGGGAA---ATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatatagcactatttttctacatg-catatgctctaatatcttttcgttttttgaaagaaatcatgagttttactctatgatcgaagacttggaagt-

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|20513053|gb|BQ280239.1|BQ280239

EST:     CTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: CTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|211542101|gb|FL388067.1|FL388067

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTTAGA-GGTGGAGCAGACAAGGATGAAGAAGATGC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTT-AGAAGGTGGAGCAGACAAGGATGAAGAAGATGC

EST: gi|60346930|gb|DN213903.1|DN213903

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|30087804|gb|CB886010.1|CB886010

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|60355695|gb|DN222668.1|DN222668

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|113704194|gb|EE681698.1|EE681698

EST:     CGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGTATGAAGAAGATGCC
genomic: CGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|74034821|gb|DT535312.1|DT535312

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|9953126|gb|BE639709.1|BE639709

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|33091656|gb|CF051650.1|CF051650

EST:     CATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: CATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|14243333|gb|BG840971.2|BG840971

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|211035290|gb|FL425632.1|FL425632

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAG-KKTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|21394198|gb|BQ538628.1|BQ538628

EST:     TGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: TGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|31558361|gb|CD527573.1|CD527573

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|60338870|gb|DN205843.1|DN205843

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|37398879|gb|CF636759.1|CF636759

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|20300887|gb|BQ163830.1|BQ163830

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCCAGACAAGGGATGAAGAAGATG
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGC-AGACAAGG-ATGAAGAAGATG

EST: gi|32797543|gb|CD949779.1|CD949779

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|19058225|gb|BM736892.1|BM736892

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

EST: gi|109179476|gb|EC380017.1|EC380017

EST:     ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAG                         GGTTTGAAGAAAGCTGTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC
genomic: ATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCC

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), 48 (downstream exon)
Score: 334

TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagta ... aacacaacagGGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCCGAGGGAAGACGGGCTTTACATTTTGCATGTGGCTATGGTGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 334

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 295

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 267

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgagtaaaagtgtctttttatctgacttctaaaggaatgaacagtgttagcatatgtgagttggggcctgtttctgtagatagatttatgttataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaggaat