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

...taaagctcttctttttttcattttagacagcccatttgacacttattatatgaacattgtacatatttgatatcccaacgagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA

Basic information

species	Zea mays
transcript	GRMZM2G005459_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g71200.1 (Oryza sativa), 3'ss of exon 5

taaagctcttctttttttcattttagacagcc-catttgacacttattatatgaacattgtacatatttgatatcccaacgagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA
 | | ||  | | |   | || |||  |||   |||         |          ||| | |||   | ||||   ||     ||| || |||||  ||||| ||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||||||||||| ||||| |  ||   |||| |||| || |
gataccttgtgtctgcattatattatccagttacatcccttctcaaaccccacgttatttttcatgaat-atattataatctcttctgatttatttgttagGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGCCGATACAGAAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTA

upper sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5

taaagctcttctttttttcattttagacagcccatttgacacttattatatgaacattgtacatattt-gatatcc-caac--gagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA
      | ||  |    ||||    ||||       ||| | |  | |   ||  | | ||   |||  |||||   |||   ||  | |  | | ||   |||||||| || || || || |||||||||||||||||||| ||||||||||| || ||||| | ||| || ||||| ||||| ||    ||| || ||||  
----tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC

upper sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 5

taaagctcttctttttttcattttagacagcccatttgacacttattatatgaacattgtacatattt-gatatcc-caac--gagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA
  | | ||| |  |  | |||   ||| || |    ||| | |  | |   ||  | | ||   |||  |||||   |||   ||  | |  | | ||   |||| ||| || || || || |||||||||||||||||||| |||||||||||||| ||||| | ||| || ||||| ||||| ||    ||| || ||||  
--atgttctccactcatacatgagagaaagtc--actgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGATTCGAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGGCAAGCTCGTAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC

upper sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4

taaagctcttctttttttcattttagacagcccatttgac-acttattatatgaacattgtacatatttgatatcccaacg----agctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA
   ||||  || |   |    |  | |  | | |||  |   || | |  ||||  ||  || ||   |   ||  |||       | | |  |   || |  ||||||| || || || ||||||||||||||||| ||||| |||||||||||||  ||||| |  || |||||||| ||||| ||  | ||| | || ||  
--tagctactcatacat--gatgaaaattgtcaattaaattgctaactcaatgattat-ataaattcatacaattgcaatctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC

upper sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 5

taaagctcttctttttttcattttagacagcccatttgacacttattata-tgaacattgtacatatttgatatcccaac-gagctctaatatattttg---tagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA
       |    || | | |  |  || ||   ||||    ||||| | | || | |   |   |   ||||     | | || |  || | | | |||   |||||||| || || ||  | |||||||||||||||||||| ||||||||||| || |||||||| || || |||||||| || |||  |||| || | || |
-----tccccagttctgtgaagtgggatagtggatttctgccttataaaaatggagaagttgattcgatgattggttatctgaccattagtttctgttgcattagGGTTCAAGTGTTCCTCTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGGAAGGCTCAGAAAGCTCAATCTCAGGCATCTAATTTGCCAA

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|148934646|gb|EC878697.2|EC878697

EST:     ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAG                         GGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG
genomic: ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG

EST: gi|13178261|gb|BG349519.1|BG349519

EST:     GCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAG                         GGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG
genomic: GCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG

EST: gi|13178262|gb|BG349520.1|BG349520

EST:     CTCTAAACGGGAAGCACAAAATAGAG                         GGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG
genomic: CTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG

EST: gi|149074524|gb|EE162922.2|EE162922

EST:     ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAG                         GGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG
genomic: ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG

EST: gi|148974793|gb|EE025615.2|EE025615

EST:     ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAG                         GGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG
genomic: ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG

EST: gi|101391173|gb|EB817520.1|EB817520

EST:     ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAG                         GGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG
genomic: ATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGG

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: 175

CTGGCTGTGCCTTCATTAAATATCAAACAAAAGATCAAGCATTGGCAGCTATTGAAGCTCTAAACGGGAAGCACAAAATAGAGgtctgtcaaa ... tattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 104

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

Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 36

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttatatgaacattgtacatatttgatatcccaacgagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA

                                     ctctaat  putative branch site (score: 36)
                                      tctaatatattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaagctcttctttttttcattttagacagcccatttgacacttattatatgaacattgtacatatttgatatcccaacgagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - -tttcatt
- - - - - - - - - - - - - - - -ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacga