Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattgggttttttagtctcctgtttgcatttatttttttagcactgaattctgtcatctttttgaag

Basic information

species Zea mays
transcript GRMZM2G134582_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134582_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 5'ss of exon 3
---------------------------------------ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattggg---ttttttagtctcctgtttgcatttatttttttagcactgaatt-ctgtcatctttttgaag
                                       |||||||| || ||||||||||||||||||||||||||||||||||| |||||| |||||||||| | | |  ||||||  | | ||   | | ||| |||  |  |  ||| |  |  |||||  || | |  ||||||| ||  |||||
CATTCGCACAGAATCTTATTTGGACACGTTTTCTTTCAGATTCCTGTTCTAGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggaattggagttctcttaatctttttctatcatat-ctgatttagttctaagtcactgtcattttcctgaag

upper sequence: GRMZM2G134582_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12800.3 (Oryza sativa), 5'ss of exon 1
---------------------------------------ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattgggtttttt--agtctcctgtttgcatttatttttttagcactgaattc-tgtcatctttttgaag
                                        | ||| | || |||||||||||||||||||||||||| |||||||| |||||| |||||||||| | | |  ||||||  |||  ||| |||  |  ||  | | |  |||  ||  |||||  || | ||| | |||| ||  |||||
CATTTGCACAGAATCTGATTTGGACACGTTTCCTTTCAGGTCCCTATTCTAGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaag

upper sequence: GRMZM2G134582_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g12800.2 (Oryza sativa), 5'ss of exon 3
ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattgggtttttt--agtctcctgtttgcatttatttttttagcactgaattc-tgtcatctttttgaag
 | ||| | || |||||||||||||||||||||||||| |||||||| |||||| |||||||||| | | |  ||||||  |||  ||| |||  |  ||  | | |  |||  ||  |||||  || | ||| | |||| ||  |||||
GTCCCTATTCTAGAGACTCCTGATGGTCCTGTTTTTGAAAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggattccgttcttttaatccttttctctctattgcttgatttagttctaagttcctctcattttcctgaag

upper sequence: GRMZM2G134582_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G57720.1 (Arabidopsis thaliana), 5'ss of exon 4
ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattgggttttttagt--ctcctgtttgcattt----atttttttagcac--tga--attctgtcatctttttgaag
 ||||||| || ||||||||||| |||||  | |||||||||||||| |||||  |||||||||    || |  |    |   ||  | | || |   | ||| | |  |  |    |||  ||    |   |||   || ||| |||    |  ||
GTTCCTGTGCTTGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgta---taacttcatttccttctgtttctctttgatgcacctatctataacttggtattaattggatatgatgattgttttgttatcccccttcag

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|211419497|gb|FK986932.1|FK986932
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|67025845|gb|CO454594.1|CO454594
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211299931|gb|FL223399.1|FL223399
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTS-AAGATATG                         NNACNCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211419502|gb|FK986937.1|FK986937
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211269909|gb|FK986924.1|FK986924
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTSCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|17930924|gb|BM267884.1|BM267884
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|15053873|gb|BI359418.1|BI359418
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211269911|gb|FK986926.1|FK986926
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|31354444|gb|CD438801.1|CD438801
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|15209068|gb|BI430952.1|BI430952
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|50333934|gb|CO529060.1|CO529060
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211269910|gb|FK986925.1|FK986925
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211419500|gb|FK986935.1|FK986935
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTS-AAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|21891605|gb|BQ744818.1|BQ744818
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211244386|gb|FL238837.1|FL238837
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211269915|gb|FK986930.1|FK986930
EST:     GGAGACTCCTGATGGTCCTGTTTTYGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|60398445|gb|DN231261.1|DN231261
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211512831|gb|FL354907.1|FL354907
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|31354453|gb|CD438810.1|CD438810
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|67020169|gb|CO448918.1|CO448918
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|211269908|gb|FK986923.1|FK986923
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGAATCTTCACTGATTGAT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGA-TCTTCACTGATTGAT
EST: gi|60399613|gb|DN232423.1|DN232423
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|6020992|gb|AW065920.1|AW065920
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
EST: gi|14529440|gb|BI096573.1|BI096573
EST:     GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATG                         TTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT
genomic: GGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATT

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: 337

ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 410

ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 335

ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaa ... ctttttgaagTTACTCGCTTGAAGGCTGATAACCCACTTTATGGATCTTCACTGATTGATTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattgggttttttagtctcctgtttgcatttatttttttagcactgaattctgtcatctttttgaag

- - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA