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

gtaaccatattttgtttcacttcatattttgaatccttgttgaagatactagcaataaattgacacatgatatgaatctgtgcgttctaactacgctcatttaatttgttctcaatatgcctttagtctcaagtccctagcgagtcataggtagaatatctttgaacttaccttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG

Basic information

species	Zea mays
transcript	GRMZM2G006937_T01
intron #	15
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006937_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g04750.3 (Oryza sativa), 3'ss of exon 10

gtaaccatattttgtttcacttcatattttgaatccttgttgaagatactagcaataaattgacacatgatatgaatctgtgcgttctaactacgctcatttaatttgttctcaatatgcctttagtctcaagtccctagcgagtcataggtagaatatctttgaacttacc---ttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG-------------------
                                                                                                    | |  || |  | ||||  || |||   | ||        |  |  | | ||  |   | |    | || ||   |  |       |  |||   ||| |||| ||||||||  |||||||||| | |||||| || |||||||| || |||||||||||  ||||||||||||||||||||                   
----------------------------------------------------------------------------------------------------tgaggttttgtttaatacaccattaaattaaaaggtaattcttggaa-atgtcaaccttttgcagatttccccactgctttttttttataatatcaaacagGTTTATGTAAACATCAAAGGTGATCATGCTCATGCAGTGAATACTGCTTGGGCAATGCTGACTTTAATTTATGCTGGACAGGTATTTTTTTTATTGTCAA

upper sequence: GRMZM2G006937_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g04750.2 (Oryza sativa), 3'ss of exon 10

gtaaccatattttgtttcacttcatattttgaatccttgttgaagatactagcaataaattgacacatgatatgaatctgtgcgttctaactacgctcatttaatttgttctcaatatgcctttagtctcaagtccctagcgagtcataggtagaatatctttgaacttacc---ttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG
                                                                                                    | |  || |  | ||||  || |||   | ||        |  |  | | ||  |   | |    | || ||   |  |       |  |||   ||| |||| ||||||||  |||||||||| | |||||| || |||||||| || |||||||||||  ||||||||||||||||||||
----------------------------------------------------------------------------------------------------tgaggttttgtttaatacaccattaaattaaaaggtaattcttggaa-atgtcaaccttttgcagatttccccactgctttttttttataatatcaaacagGTTTATGTAAACATCAAAGGTGATCATGCTCATGCAGTGAATACTGCTTGGGCAATGCTGACTTTAATTTATGCTGGACAG

upper sequence: GRMZM2G006937_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g35710.1 (Oryza sativa), 3'ss of exon 15

gtaaccatattttgtttcacttcatattttgaatccttgttgaagatactagcaataaattgacacatgatatgaatctgtgcgttctaactacgctcatttaatttgttctcaatatgcctttagtctcaagtccctagcgagtcataggtagaatatctttgaacttaccttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG
                                                                                                  || | ||  |     ||  ||   |  |   ||| |   ||   |  |||  | |  || || |   ||| |  |||       |||  || | ||| |||| || |||||  | |||| ||| |  ||||| || |||||||| |||||||||||| | |||||||||| ||| ||||||
--------------------------------------------------------------------------------------------gaagaaatcttatgagggaagaagttggact--ggtgcaaatttttataaatccatttggaagatttcgtc--actgatttttattttttatg--ataccaaacagGTTTACGTAAACATTAAAGATGATCAAGCTCATGCAGTGAATACTGCCTGGGCAATGTTAGCTTTAATTTGTGCAGGACAG

upper sequence: GRMZM2G006937_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g04750.1 (Oryza sativa), 3'ss of exon 10

gtaaccatattttgtttcacttcatattttgaatccttgttgaagatactagcaataaattgacacatgatatgaatctgtgcgttctaactacgctcatttaatttgttctcaatatgcctttagtctcaagtccctagcgagtcataggtagaatatctttgaacttac---cttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG
                                                                || |  |   ||| | | |    |    |||    || |  || |  | ||||  || |||   | ||        |  |  | | ||  |   | |    | || |   ||  |       |  |||   ||| |||| ||||||||  |||||||||| | |||||| || |||||||| || |||||||||||  |||                 
--------------------------------------------------------------ggac-tagtgcaaatttctacaaattt-taacgtattttgaggttttgtttaatacaccattaaattaaaaggtaattcttggaa-atgtcaaccttttgcagATTTCCCCACTGCTTTTTTTTTATAATATCAAACAGGTTTATGTAAACATCAAAGGTGATCATGCTCATGCAGTGAATACTGCTTGGGCAATGCTGACTT-----------------

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|60352032|gb|DN219005.1|DN219005

EST:     AGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAG                         GTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG
genomic: AGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG

EST: gi|4681216|gb|AI629886.1|AI629886

EST:     AAGTCATATCGCTATTGAAACTCAG                         GTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG
genomic: AAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG

EST: gi|33099602|gb|CF059562.1|CF059562

EST:     ACTGGTGGATGGGGAGAAAGCCATATCGCTATTGAAACTCAG                         GTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG
genomic: ACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG

EST: gi|32863035|gb|CF002717.1|CF002717

EST:     AGCTCAGTACTGGTGGATGGGGAGAAAGCCATATCGTTATTGAAACTCAG                         GTGTATGTAAATCTCAAAGGTGAC
genomic: AGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGAC

EST: gi|211245891|gb|FL430652.1|FL430652

EST:     AGCTCAGTACTGGTGGATGGGGAGAAAGCCATATCGCTATTGAAACTCAG                         GTGTATGTAAATCTCAAAGGTGMCCGTGCTCACGCTGTGAATACCGCCTGG
genomic: AGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG

EST: gi|166657991|gb|EG244196.1|EG244196

EST:     AGCTCAGTACTGGTGGATGGGGAGAAAGCCATATCGCTATTGAAACTCAG                         GTGTATGTAAATCTCAAAG
genomic: AGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAG

EST: gi|211357851|gb|FL385254.1|FL385254

EST:     AGCTCAGTACTGGTGGATGGGGAGAAAGCCATATCGCTATTGAAACTCAG                         GTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG
genomic: AGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 43

CAAGAACAGCCCTTGCATACGGAAAGCATGCCACTTCATATTGTCGAAGCAGCTCAGTACTGGTGGATGGGGAGAAAGTCATATCGCTATTGAAACTCAGgtaaccatat ... tcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

Block sizes: 29 (upstream exon), 39 (downstream exon)
Score: 2

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtcataggtagaatatctttgaacttaccttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG

                     aacttac  putative branch site (score: 109)
           aatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccatattttgtttcacttcatattttgaatccttgttgaagatactagcaataaattgacacatgatatgaatctgtgcgttctaactacgctcatttaatttgttctcaatatgcctttagtctcaagtccctagcgagtcataggtagaatatctttgaacttaccttttcccaccatgcaatcctaaatagGTGTATGTAAATCTCAAAGGTGACCGTGCTCACGCTGTGAATACCGCCTGGGCAATGCTCGCTTTAATTTATGCTGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA