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

gtcggggtttattatatttgtcccattaaaatttaatttctttgttctaatttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC

Basic information

species	Zea mays
transcript	GRMZM2G565140_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 4

-------------gtcggggtttattatatttgtcccattaaaatttaatttctttgttctaatttgctggagcacgttag-caatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
                |   ||| |||| |||| ||   |  |  |||| | ||   || || | |     |   | |||    | |||||  ||   |  |||| |||||||||||||| || |||||||| ||||||||||||||||| ||||| ||| |||||||  |||  ||| |||| |||||||| ||  |||| |
gtgaatgtagtttactgtcattttttatgtttgaccatatcgaccttaaatactaatttttactata---aaatgctttaaattaattgttcattcatttcagGAGCATGCAAAAGGTGGTAAATGCATTGTATTTACACAAACAAAAAGAGATGCTGATCGATTGTCCTACACCATGGGTCGGAGTTTCCAGTGCCAGGCCC

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4

-------gtcggggtttattatatttgtcccattaaaatttaattt------ctttgttcta-atttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
             ||  |   ||||| |      ||||  || ||       |||  | ||  ||||  |   |     ||   || | |    || || ||||||||||||||||| || |||||||||||||| || ||||||||| | ||||| ||| |||| ||| | |  |||    ||||| |  ||||||||||  
ggactaaaagatagtaaaccctatttttatttagaaaaactagttaaggaaacttcttgctggatttttttttgtctcctaaagatatatc--ctttgt-tagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4

-----gtcggggtttattatatttgtcccattaaaatttaatt--------tctttgttcta--atttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
           ||  |   ||||| |      ||||  || ||        | ||||||  |  ||||  ||   | |  ||   || |||    || || ||||||||||||||||| || ||||| |||||||| || ||||||||| | ||||| ||| |||| ||  |    |||    ||||| |  ||||||||||  
ctaaaaagatagtagaccctatttttaattagaaaaactagttaaggaagctttttgttaaaggattttttgtctctc-ctaaagatatgtc--gtttgt-tagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4

------------------------------------gtcggggtttattatatt---tgtcccattaaa--attta---atttctttg---ttctaatttgc---tggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
                                    ||     ||| |  ||||   |  |  | |||   ||||    |||| || |   || | | |||    ||||    ||||  ||| |   | || | || |||| ||||| ||||| || || |||||||||||||||||||||||| | ||||| ||| |  | ||| |     ||  | |||| ||| ||||||| ||  
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4

-----------------------------------------------------------------------------------gtcggggtttattatatttgtcccattaaaatttaatt---tctttgttctaatttgctggagca-----cgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
                                                                                    |     |     |||  |  ||  ||  | ||||  |   ||||  || ||  |   |  ||       | ||||||   |   ||| |    |||||||||||||||||||| || || |||||||| || ||||||||| | ||||| ||| ||||| || |   ||||    |||  |||  ||||||||| |
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC

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|32842833|gb|CD982514.1|CD982514

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842842|gb|CD982523.1|CD982523

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842824|gb|CD982505.1|CD982505

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842589|gb|CD982270.1|CD982270

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842460|gb|CD982141.1|CD982141

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842456|gb|CD982137.1|CD982137

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842583|gb|CD982264.1|CD982264

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842809|gb|CD982490.1|CD982490

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842651|gb|CD982332.1|CD982332

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842391|gb|CD982072.1|CD982072

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842737|gb|CD982418.1|CD982418

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842485|gb|CD982166.1|CD982166

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842566|gb|CD982247.1|CD982247

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842765|gb|CD982446.1|CD982446

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842619|gb|CD982300.1|CD982300

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842579|gb|CD982260.1|CD982260

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842750|gb|CD982431.1|CD982431

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GACCATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32842646|gb|CD982327.1|CD982327

EST:     TCTCTTCGGAAAACCGTGAAAACCCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

EST: gi|32841848|gb|CD981529.1|CD981529

EST:     TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAG                         GAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT
genomic: TCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGAT

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: 181

GTTGGTGAGGATGACCAAAAGCTGGCTGAAGGAATTAGTCTGCTCTCTGTCTCTTCGGAAAACCGTGAAAAACCAGCTGTTCTTGGGAAATTGATTAAGgtcggggttt ... tttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 101

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatttctttgttctaatttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC

          ttctaat  putative branch site (score: 151)
                                         tttgtttc  putative PPT
          ttctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggggtttattatatttgtcccattaaaatttaatttctttgttctaatttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT