ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctgtccacatttgttctgtaatattagcttagtatgtgcaattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcag

Basic information

species	Zea mays
transcript	GRMZM2G118731_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 5'ss of exon 2

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctgtccacatttgttctgtaatattagcttagtatgtgcaattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcag
 |||||||| |||||||| ||||  ||||||||||| |||||||| ||| | ||||||||||| |||||||| ||||||||||||||||||||||||||||| ||    |  || |   |||||   ||||| |  || | | || || ||| ||| |  |       | ||||| |||  | |||   | | |||
GCTTGGTGTATCTAAGACAGCAACCCAGGATGAGCTGAAGAAAGCGTACCGTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctgg---ggacaaaca-gttct---atatttgtctactct-tg-aactgttggtttggtttggttgacgttttacttttt-atggcttggtcag

upper sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 5'ss of exon 2

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctgtccacatttgttctgtaatattagcttagtatgtgcaattgtaggtgt---tctcatcgccaggttttccttgatgatgaacttggcag-
|||||| || || || |  || | ||| ||||| || ||||| ||||| | ||| ||||||||||| ||||| || || |||||||||||||| ||||||||   | ||    |   | |  |   ||    | | ||       |||||  || |     |    |    || | | |  ||   |||||||   |   
TCTTGGAGTTTCAAAAAATGCCAATCAAGATGAACTGAAGAAGGCATATAAAAAGGCTGCCATAAAGAACCACCCAGACAAGGGTGGAGACCCGGAGAAGgtaaatccttataaacctagaccaccaaagccaccataaccaccacaattacagttacaaattctttttaaagatctcctatgtgaatgaactacccgag

upper sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S100_36V6.1 (Physcomitrella patens), 5'ss of exon 1

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttg-------ttctgtccacatttgttctgtaatattagcttagtatgtgcaattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcag-
 || || ||||| |||| |||    ||||||||||| ||||| || ||||| || || || || || || ||||||||||||||||||||||| ||||||||  |       ||  ||      | | ||| |     ||| |   |    |       |||| | | | ||  ||||   |    ||||  || ||    || 
GCTCGGGGTGTCGAAGAGCGCGTCGCAGGATGAGCTGAAGAAGGCGTACAGGAAGGCGGCAATTAAGAATCATCCTGATAAGGGTGGAGACCCGGAGAAGgtacgatagtgttttagttggggatcggtctctgtgtctagttccttggccgtgg--aaaggtctgcccgtcctcaggacatatccgatg--gacctacagagt

upper sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S174_37V6.1 (Physcomitrella patens), 5'ss of exon 1

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttc-tgtccacat-----ttgttctgtaat--attagcttagtatgtgc--aattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcag--------------------------------------------------------------
||| || ||||| ||||  |||   || |||||||| |||| ||| ||||| || || || || ||||||||||| ||||||||||| ||||||||||||||  |||  |||    ||     ||| |||||| |   | ||      | ||||  |||  |   | || | |  |   |   |||   ||    |  ||| |  |                                                              
TCTAGGGGTGTCGAAGAGTGCATCGCAAGATGAGCTGAAGAGAGCTTACAGGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggtgtttggatgggcgttgctctgtagtttgtcagtgagccacgtgcggaatgcttaatattttgaa-gttggcacttcaaggagatcgtgctttgtggagtcggtgttctcgtttgtaaatatcatatatacctgcttacttgagtgatctttttcgcag

upper sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S174_97V6.1 (Physcomitrella patens), 5'ss of exon 1

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctgtccacatttg-ttctg--taatattag---cttagt-atgtgcaattgtaggtgttctcatcgccaggt------------tttccttgatgatgaacttggcag-----------------
 ||||| |||  ||||  ||||   | ||||||||||||||| || ||||| || ||||| || || ||||||||||| || |||||||| || ||||||||  |      |   ||||| |||||  ||  | | |    ||||   | ||  ||||| |  || |    |   ||||            | |  ||   ||||||||  |  |                 
CCTTGGGGTGGGTAAGGGCGCATCGCCGGATGAGCTTAAGAAGGCGTACAGGAAGGCTGCAATTAAGAACCATCCTGACAAAGGTGGAGATCCAGAGAAGgtagggctacgctctatttgattctgagtaggacttgagttttagccgtttgggattgtcgacgtgcagcacagaaggtgcagatgtgagatgttgttatagatgaactaagacgtagctttctctctgcag

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|76909048|gb|DV163196.1|DV163196

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|76293182|gb|DV032750.1|DV032750

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|211439726|gb|FL188864.1|FL188864

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAAAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|211003695|gb|FL188865.1|FL188865

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAAAAA                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|87152878|gb|DY397667.1|DY397667

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|33094456|gb|CF054450.1|CF054450

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|148964320|gb|EC905716.2|EC905716

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|31348685|gb|CD433042.1|CD433042

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAAAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|32932432|gb|CF037244.1|CF037244

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTCAAAGAGCTGTCCCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|91877653|gb|EB407610.1|EB407610

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|148931484|gb|EC874496.2|EC874496

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|149037356|gb|EE155375.2|EE155375

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|148955629|gb|EC901294.2|EC901294

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|18963675|gb|BM660568.1|BM660568

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         GTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGGGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|18964089|gb|BM660803.1|BM660803

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

EST: gi|13150523|gb|BG320845.1|BG320845

EST:     GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAGBTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG
genomic: GAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGG

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: 139

TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctg ... aacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGGGAGATCTATGACCAGTATGGAGAAGATGCCCTTAAGGAAGGAATGGGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttctgtccacatttgttctgtaatattagcttagtatgtgcaattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA