ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtattatagacaaagcacttttgatatttttcacataccataattacctaacccagtattactaatatttgcag

Basic information

species	Zea mays
transcript	GRMZM2G153332_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 4

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtattatagacaaagcacttttgatatttttcacataccataattacctaacccagt--attact-aatatttgcag------
  || |||||||||||| ||||| || ||||| |||||||| |  ||||| || || ||||| || |||||||||||||| ||||| ||||||||||||||||||||  | | ||| | |   |||||| | |||  | |    |  | |   |  |   |  ||||||  |||| |  |       
AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacgacaaacagaac-tatttgatctcttttgcctgttgtgttaaaaaagactgatgcattacttgatatatcaacgtgcag

upper sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G07860.1 (Glycine max), 5'ss of exon 5

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtg--------------tattatagacaaagcacttttgatatttttcacataccataattacctaacccagtattact--aatatttgcag--------------------------------------------------------------------
 | |  || ||||||||||||   ||||| || ||||||||||  ||||| ||| ||||||| |||||| | |||||||| |||||| ||||||||||||||  |              | || ||  |  |   | |||   ||| ||  || |  | |  |   |   | ||   || |    | ||| ||                                                                     
CAAGACGGAGGATGGATTGCACGAATTGCAGCTTTACTTGTGGGTGAGGATCCAACACAGTCGTATGCTCTCATATGTGGTAACTGCTATATGCATAATGgtaagggggctagatttgatcttgtatgctcatgtccttttgcattatt-gcagaataaagatgattgtactagggctattttgttttttacaatagaccatgttaatagatgaatacaacagtcaaaaaaattgtattcttatctgcttattttctttcag

upper sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G07930.1 (Glycine max), 5'ss of exon 5

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtattatagacaaagcacttt-tgatatttttcacataccataattacctaacccagtattacta-atatttgcag------------------------------------------------------------------------------------
 | | ||| ||||||||||||   ||||| || ||||||||||  || |||||| |||||||||||||  | ||||| || |||||| ||||||||||||||  |     ||||        ||| ||||  | | |   | |  | ||| |  ||   || || | |  | |  |||                                                                                      
CAAGATGGAGGATGGATTGCACGAATTGCAGCTTTACTTGTGGGCGAAGACCCAACACAGTCATATGCGCTCATATGCGGTAACTGCTATATGCATAATGgtaagggggctagatttgatcttttatgatcatgtccttttgcatttattgcagaataaag-atgattgtacaagtgctattttgtttttttacaatagaccatgttaatagatgaatacaacagtaaaaaaatgtgtattcttatctgcttattttctttcag

upper sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0432g00020.t01 (Vitis vinifera), 5'ss of exon 2

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgta-----------------ttatagacaaagcacttttgatatttttcacataccataattacctaacccagtattactaatatttgcag-------------------------------------------------------------------
 ||| ||| |||||||||||    ||||||||  |||||||||  ||||| ||| || |||| |||||  | |||||||| ||||| |||||||||||||||  ||                  |||                                                                                                                                       
CATGATGGGGGATGGATTGCTCGAATTGCTGCACTACTTGTGGGGGAGGATCCAACAGAGTCTTATGCACTTATATGTGGAAACTGTCATATGCATAATGgtaagtggagtgaggacctcatccttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaagtagttttgtcctgtttttgtttttgtgcag

upper sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0215g00090.t01 (Vitis vinifera), 5'ss of exon 5

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgt--gtgtattatagacaaagcacttttgatattt-ttcacataccataattaccta-acccagtattactaatatttgcag------------------
 ||| ||| |||||||||||    ||||||||  |||||||||  ||||| ||| || |||| |||||  | |||||||| ||||| |||||||||||||||  ||| | |   |||      |||   | || | ||       ||  ||||| |     ||  ||||||  | |   |                    
CATGATGGGGGATGGATTGCTCGAATTGCTGCACTACTTGTGGGGGAGGATCCAACAGAGTCTTATGCACTTATATGTGGAAACTGTCATATGCATAATGgtaagtggagtgaggacctcatccttacaaaatgtatttctgcttcaggattacttttgttcatcattacttttttcctccatgtcccctactgttaatt

upper sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0033g01150.t01 (Vitis vinifera), 5'ss of exon 6

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtattatagacaaagcacttttgatatttttcacataccataattacctaacccagtattactaatatttgcag--------------------
 ||| ||| |||||||||||    ||||| || || |||||||  ||||| ||| |||||||||||||  | ||||| || |||||||||||||| ||||||         |     || | | || | ||  || ||  |||   | | || |  |     ||  | |||| | |||                    
TATGATGGGGGATGGATTGCTCGAATTGCAGCATTGCTTGTGGGTGAGGATCCAACACAGTCATATGCGCTCATATGCGGGAACTGCCATATGCACAATGgt---------aagtggagtagtattcacatccttaacccacctggacttccaactcttagttttgtcatatcttcaggggtctttggtttggtgcag

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|71774634|gb|DR972512.1|DR972512

EST:     CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATG                         GCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT
genomic: CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtatta ... atatttgcagGCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT

EST: gi|67025071|gb|CO453820.1|CO453820

EST:     CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATG                         GCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT
genomic: CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtatta ... atatttgcagGCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT

EST: gi|60338605|gb|DN205578.1|DN205578

EST:     CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATG                         GCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT
genomic: CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtatta ... atatttgcagGCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT

EST: gi|32846154|gb|CD985835.1|CD985835

EST:     CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATG                         GCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT
genomic: CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtatta ... atatttgcagGCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT

EST: gi|93017027|gb|EB642547.1|EB642547

EST:     CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATG                         GCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTATTACTGCCCACATT
genomic: CCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtatta ... atatttgcagGCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATT

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: 45 (upstream exon), 48 (downstream exon)
Score: 32

GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtatta ... atatttgcagGCTTGGCCCGAAAGGAAGATTATCCGCATGTTACCTACTACTGCCCACATTGTCATGCATTAAACACATCAAAGCAGTCCATGTGGCAATACTCGGGCTC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 32