ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGCCCGCCTTCGGTTCCCTCGGCTGCGCGCGAGGATTTGATGGCTCAGGTCGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaacgcctcctccgcacatagtttaccaatttatttgcttgttatgcgagattctactaacatgagaaggttagcttaggatacgtgcagagtg...

Basic information

species	Zea mays
transcript	GRMZM2G009575_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G009575_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g39462.1 (Oryza sativa), 5'ss of exon 1

GGCCCGCCTTCGGTTCCC-TCGGCTGCGCGCGAGGATTTGATGGCTCAGGTCGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgta-aattaacgcctcctccgcacatagtttaccaatttatttgcttgttatgcgagattctactaacatgagaaggttagcttaggatacgtgcagagtg
 | |  ||  | |  ||| ||| | |  |||   |||| | | |  ||| ||||||||||||| || ||||| || ||||||||||||||| |||| ||||||| |||   ||  ||| |  | |      | |    |  | |||||  |||   ||      ||| | ||        |||     | | ||      ||
-GACGACCCGCAGCACCCGTCGTCCGGTCGCCCCGATTCGGTTGACCAGCTCGATCAGTTCCTCCGGGAGGCGCTCGAGAAGCCGAGGGAGCGGCTCTCTGgtataatattcgaatccccatcccccctgctgcaccctcctctgcttcgtatcataggcctagctaccctgtttctacaagca-gtaacaagtcgcacttg

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|149014850|gb|EE044558.2|EE044558

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|91876677|gb|EB406634.1|EB406634

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|71429166|gb|DR810216.1|DR810216

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|101390325|gb|EB817096.1|EB817096

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCCTAGGTTT
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCC-TAGGTTT

EST: gi|91875337|gb|EB405294.1|EB405294

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|37417682|gb|CF646498.1|CF646498

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|76287697|gb|DV027265.1|DV027265

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|149099408|gb|EE185448.2|EE185448

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|148935275|gb|EC879314.2|EC879314

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|91050262|gb|EB160680.1|EB160680

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|148950309|gb|EC895868.2|EC895868

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

EST: gi|211113329|gb|FL110893.1|FL110893

EST:     CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTG                         TGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA
genomic: CGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTA

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: 347

GGCCCGCCTTCGGTTCCCTCGGCTGCGCGCGAGGATTTGATGGCTCAGGTCGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaac ... ctgtctgcagTGCTAAGAATGGAGCAAGAAATTTTGAAGTTCATTGGTGACCCTAGGTTTACAGAGTATGAATTCAATGGTCTTCCAACTTCATATTTGCGTCTCGCTGC

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 231

Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 207

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 345

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCCGCCTTCGGTTCCCTCGGCTGCGCGCGAGGATTTGATGGCTCAGGTCGATCAGTTCCTACGAGAGGCTCTAGAGAAGCCGAGGGAGAGGCTTTCTGgtaaattaacgcctcctccgcacatagtttaccaatttatttgcttgttatgcgagattctactaacatgagaaggttagcttaggatacgtgcagagtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG