ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag

Basic information

species	Zea mays
transcript	GRMZM2G042074_T02
intron #	18
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||| ||||||||| |   | ||  | ||||| || | |||   || | |   |   ||||   | |    |    ||  | ||  || |  |||  || ||   | |||                                         
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaa--attgtaat-tgatcaatca-caacgcctttctgaattccctgtg--atgtttgctttctagtt-tatcttcttcatcttgtgtt---gtatag----------------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 21

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||| || || ||||  |||||||||||||| || ||||| ||||||||| | || ||||| || ||||| || ||||||||   |          | | ||| |   |  || | ||   |||||   |   |    ||   | || || |  ||                                                                
TGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagcctt----------ttaaccaagggta--ttgtgttgtattgattcattgaatataactttactagctttgtttcag-------------------------------------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 19

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||||||||||||||  || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| || |||||  || |||  |                | |  |||  ||| |||  | |||   |      |  ||| ||| ||  || |  | |   |  |||||   | || | |  ||| ||                          
TGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgttggt-ataacat---------------atatcttccttttttttactttgttttaaatattctaaatttctttacatt-ttgaccgttttataatgtccatttgtgttgtcagtt--------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 22

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||||||||| || |  || |||||||| ||||| || || || ||||||||||||||||| |||||||| ||||||||   || ||  |      |  |  ||   |  ||    ||   ||   || ||     | |    | | |   || ||| |  |   | ||| |   |||                                          
TGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgttgctt-tatcatgtcatttgtttatattcctttgaagttctcttttcctttattttaa-atattatttttaatactttttagaattcatatgagc-cattt----------------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA06G17940.1 (Glycine max), 5'ss of exon 23

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||| || ||||||| |||||||||||||||||| |||||||||||||||||||| || || || ||||| ||||| |||||   |  | || |     | | |      | || ||| |   |  ||| |  |  |  |    | | |  |||| || |  ||  ||||                                                  
TGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagcctt--ttgtataaatgttcttagtttgtatcaattcaacag--ctgaaaaataaatcagtgaaaac--tagtatggct-tcttgtatag------------------------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA04G37050.1 (Glycine max), 5'ss of exon 6

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||| || ||||| |  || |||||||||||||| ||||| |||||||||||||| || || || ||||| ||||| |||||   |  | |        |   | |    | || ||| || || |    |  |   ||    || |  ||||  | |    ||  ||||                                                  
TGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAAgtaagcctt--ttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagt-taaaacttgta--tggct--tcttgtatag------------------------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 19

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||||||||||||||  || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| || |||||      | |||    | | |   ||     || |   ||| |||  |  ||   |      |  ||| ||| ||  || | |   |||| |||    || | ||| || |     |                         
TGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgt------tggta----tataacatat-----atcttccttttttttcttggttttaaatattctaaatttctttacattttga---ccgttttataatatccatttgtgttgtcgga-------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 19

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| |||| || || || ||||  |||||||||||||| || ||||| ||||||||| | || ||||| || ||||| || ||||||||           || | |   | |   |  || | ||   |||||   |   | |  ||   | || || |  ||                                                                
TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagcc---------ttttaacttaagggta--ttgttttgtattgattcattggatgtaactttactagctttgtttcag-------------------------------------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 18

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccacaatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag
||| ||||||||||||| ||||  || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| ||||||||   ||       | || ||     ||   |  |||  || | ||  ||| | ||   |    | ||||| | |  |    |  |      || ||     |  ||                                    
TGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgttgctt-------tattatgtcatttgtttatcttcctttgaatttttcttttcctttatttta-aatattttttttaaaactttttacccttcatatgagccattt-----------------------------------

upper sequence: GRMZM2G042074_T02 (Zea mays), 5'ss of exon 18
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 22

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtacc------aggacaccac------aatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttttag--------------------------------
||| |||| |||||||| ||||  || |||||||| || || || || ||||||||||| || |||||  ||||||| |||||||||||||  |  | | ||   || |||  |||| || |  |    || ||   ||       | |   |||       | |  | |||  |  |||||||  | ||||| |   |  ||||| || ||  |     |||| ||||  | ||  |                                 
TGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAGgtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatcc--ttttaattcg--ccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcag

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|67017525|gb|CO446274.1|CO446274

EST:     TTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAA                         GTTGATGGCATGCTGGGAAGGCNGGAGAACCCTGNAGA-CATGAAGCCATG
genomic: TTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATG

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), 37 (downstream exon)
Score: 311

TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAGgtaagttata ... tattttttagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA

Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 480

Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 328