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

gtaagatccaccacttgactgtgaggagatataaaatctttgcattcctcaattatgtagtacagtatattttgtggctgatgttgatattttttgtctttctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC

Basic information

species	Zea mays
transcript	GRMZM2G055607_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G055607_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g44960.2 (Oryza sativa), 3'ss of exon 3

gtaagatccaccacttgactgtgaggagatataaaatctttgcattcctcaattatgtagtacagtatattttgtggctgatgttgatattttttgtctttctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC
     ||   || || || |     ||  ||| |  |||| | |  || |  ||||| |     ||  ||||| ||  | |||||| |     || || |||| |   ||||| ||||| || || | ||  ||||| | ||||||  | || ||||||||| | ||||||||||||||||||||||| ||| |||| || |||||||||
--gtaattttcctctagagta----gaattattatctcttagtacgcccctgttatggat----gtgcattttctgattcatgttgcttcaaattttccttcttccatagGGGAGAGTGTTCCTGCAATCTGGTTCGATCCTTTGTGCTTGTATCTATGCAACGGTCGGGAAGTGGATGGTTTGAGACTTTGCTGAACAGCCACCCTAAC

upper sequence: GRMZM2G055607_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5

----------------------------------gtaagatccaccacttgactgtgaggagatataaaat----ctttgcattcctcaattatgtagtacagtatattttg---tggctgatgttgatattttttgtct-ttctgc-tgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC
                                     |    ||  | ||  || | |     | ||||      |||     | ||||   | ||    |  |   || ||   ||   |   |    ||||  |||   || ||| ||||||   |||||| | || |||||||| |  |  ||||||||  | || ||||||||||| ||||||||||||||||||||  |  | |||| |||||| || 
gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttccttcttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT

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|71431673|gb|DR812723.1|DR812723

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|31441050|gb|CD510481.1|CD510481

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|76911991|gb|DV164525.1|DV164525

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATTGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|71448567|gb|DR829617.1|DR829617

EST:     ATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGC
genomic: ATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTT-ATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGC

EST: gi|88755485|gb|DY539626.1|DY539626

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|50329390|gb|CO524516.1|CO524516

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|71437590|gb|DR818640.1|DR818640

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|211132575|gb|FL461421.1|FL461421

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|28987385|gb|CB351608.1|CB351608

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATC
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATC

EST: gi|71305861|gb|DR789056.1|DR789056

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|91871874|gb|EB401831.1|EB401831

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|74241101|gb|DT649015.1|DT649015

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

EST: gi|50330184|gb|CO525310.1|CO525310

EST:     TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAG                         GGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA
genomic: TATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCA

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), 43 (downstream exon)
Score: 53

ATAGTCGAGAAGAACAAAGGGACGATATTTGCAGAAAGCCTTATGTGCCGTATGAGGAGCTCAGTTATGTGCACTTTCCAAAACCTACAAGTTATAGCAGgtaagatcca ... tctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgtagtacagtatattttgtggctgatgttgatattttttgtctttctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC

                          tgttgat  putative branch site (score: 187)
                                  ttttttgtctttctgc  CT-rich tract
                         atgttgatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatccaccacttgactgtgaggagatataaaatctttgcattcctcaattatgtagtacagtatattttgtggctgatgttgatattttttgtctttctgctgcagGGGGGAGTGCTCGTGTACTCCTGTTCGGTTCTTTGTAATCGTGTCTATGCAAAGATCGGGAAGTGGATGGTTTGAGACCTTGATGAATAGTCACCCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA