ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TATCATCACCTGCTGATGCTATGTTCATAGGCCTTGGTACTCACTATGTACCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttcttatctgtacttgctgaagaacctaaatactgtcaaaatcatctgtaatttctccattttttcagtttccttgttcatgtatattatagcccatgatggaataagtgcttgcttgcacgtctgtagattttgatggtaccttgatatctgatcttgttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G047564_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G047564_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 5'ss of exon 6

TATCATCACCTGCTGATGCTATGTTCATAGGCCTTGGTACTCACTATGTACCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttcttatctgtacttgctgaagaac--ctaaatactgtcaaaatcatctgtaatttctccattttttcagtttccttgttcatg-tatattatagcccatgatggaataagtgcttgcttgcacgtctgtagattttgatggtaccttgatatctgatcttgttttgcag
|||||||||||||||||||  | ||| | || ||||| ||||| ||||||||||| || ||  ||||  | |||| ||| |||||  ||||||||||||||||| || |  |    || ||| | || |    |||||| ||  ||| ||||| | |  | | |  |||  | |    |   ||  | || | |  ||  |                                                                           
TATCATCACCTGCTGATGCCCTTTTCTTTGGTCTTGGAACTCATTATGTACCTTCAGCGAACCTGGGACCTCTCAGGGAATCCCTCTTGAGTGCTAACTTgtatgttccgaactgttatttggtaaaaacttactaaatgctagcaagatcat-tatgttcttttaattactactagctgaatgcccctgctttgctactg---------------------------------------------------------------------------

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|71312657|gb|DR792849.1|DR792849

EST:     CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|60398946|gb|DN231762.1|DN231762

EST:     CATTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|78083152|gb|DV511545.1|DV511545

EST:     CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|71312658|gb|DR792850.1|DR792850

EST:     CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|60346890|gb|DN213863.1|DN213863

EST:     GCAAATTTGGGTTC-CTCAAGGAGTCCCTGGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: GCAAATTTGGGTTCACTCAAGGAGTCCCT-GCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|76280673|gb|DV020241.1|DV020241

EST:     CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTTTGACAGGATACAAGAA
genomic: CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|37379970|gb|CF626760.1|CF626760

EST:     CTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: CTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

EST: gi|91873503|gb|EB403460.1|EB403460

EST:     CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTT                         CACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA
genomic: CCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAA

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: 66

TATCATCACCTGCTGATGCTATGTTCATAGGCCTTGGTACTCACTATGTACCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttct ... tgttttgcagCACCAATGATCCTCATAGAGACGTTGAGTCAGTTCTGACAGGATACAAGAAAGAACCAGAGTCTGAACCACAACTAAAAAAGCTTTTGCCATATATCATT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCATCACCTGCTGATGCTATGTTCATAGGCCTTGGTACTCACTATGTACCTTCTGCAAATTTGGGTTCACTCAAGGAGTCCCTGCTGAGTGCTAACTTgtatatttcttatctgtacttgctgaagaacctaaatactgtcaaaatcatctgtaatttctccattttttcagtttccttgttcatgtatattatagcccatgatggaataagtgcttgcttgcacgtctgtagattttgatggtaccttgatatctgatcttgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG