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

...gctgtgggttgacgtctgtttgaacacttcatgaggcatatgggtattggttatattattactatatcctaactaactgctggattattcactcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAAGTGGGCCGTCGTAAGGCTGGATCTTAAGCTACCTACTACTTGCCTGAAA

Basic information

species	Zea mays
transcript	GRMZM2G056462_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 9

-gctgtgggttgacgtctgtttgaacacttcatgaggcatatgggtattggttatattattactatatccta-actaactgctggatt-attcactctt-gcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAAGTGGGCCGTCGTAAGGCTGGATCTTAAGCTA--CCTACTACTTGCCTGAAA
  | |||| |||| || |  |||           |  |||     |  | |||||    |    |   |  | | | |||||||| ||  || || ||  |||||||||||| || || ||||||||||| |||||||||||||||||||||||||| || ||||| ||||||||| | |||| ||  | | |  | |||      
gccagtggattgatgtattattg----tcatccaaatcatgccatttctcgttattgcttcgtcaagccaaatattgactgctggttttgtttaccctccgcagTGTGGTTCTTCAAGATCTGTTGCTCCTATCAAGGCTGGATTCGTTGCCCAAGTTGGTCGTCGGAAGGCTGGAACCTAAGTTAAACGTCCACCCTGCTCAG--

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|76291710|gb|DV031278.1|DV031278

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|71417947|gb|DR804264.1|DR804264

EST:     ATACCATTCTTTTTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|87155564|gb|DY400353.1|DY400353

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|60349693|gb|DN216666.1|DN216666

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|60337488|gb|DN204461.1|DN204461

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|29947496|gb|CB816686.1|CB816686

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         NGTGGTTCATCGAGGTCTGTTGCTCCCATCA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCA

EST: gi|60338551|gb|DN205524.1|DN205524

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|32933168|gb|CF037980.1|CF037980

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCGTCAAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|32936402|gb|CF041221.1|CF041221

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCGTCAAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|76291709|gb|DV031277.1|DV031277

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|29947331|gb|CB816599.1|CB816599

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|161583227|gb|EY954438.1|EY954438

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTT
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTT

EST: gi|60339292|gb|DN206265.1|DN206265

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAA

EST: gi|30031975|gb|CB833826.1|CB833826

EST:     ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG                         TGTGGTTCATCGAGG
genomic: ATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGG

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: 155

ATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAGgtaaattgtt ... actcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAAGTGGGCCGTCGTAAGGCTGGATCTTAAGCTACCTACTACTTGCCTGAAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 108

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attggttatattattactatatcctaactaactgctggattattcactcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAAGTGGGCCGTCGTAAGGCTGGATCTTAAGCTACCTACTACTTGCCTGAAA

                         aactaac  putative branch site (score: 108)
                                          ttcactctt  putative PPT
     ttatattattactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtgggttgacgtctgtttgaacacttcatgaggcatatgggtattggttatattattactatatcctaactaactgctggattattcactcttgcagTGTGGTTCATCGAGGTCTGTTGCTCCCATCAAGGCTGGATTCGTTGCCCAAGTGGGCCGTCGTAAGGCTGGATCTTAAGCTACCTACTACTTGCCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
gctgtgg
- - - - - - - tctgttt
- - - - - - - - - - - - - cttcatg
- - - - - - - - - - - - - - - - - -gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg