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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttagaaactgcattcagtgatagaatgacttgcttgaatgcttggcatgttttttgttcacatgtcctgacgccttaaaacgaattttctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
---acttagaaactgcattcagtgatagaatgacttgcttgaatgcttggcatgttttttgttcacatgtcctgacgccttaaaacgaatttt--ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
   |  || | |   ||||  || |   |||   ||  |   |  ||  | ||  |  || | ||  |||  ||  ||  ||| |  | ||||  ||    ||||| | |||||||||||||||||||| |||||||||||||| ||||||  |||||||| |||||||||||| ||||||||||| ||||||
tacaagtacagaac-cattatgttaagcaatactttatt---actctcagaatagtgattttgcagttgttttg-tgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG

upper sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
-------------------------------------------acttagaaactgcattcagtgatagaatgacttgcttgaatgcttgg---catgttttttgttcacatgtcctgacgccttaaaacg---aattttcta----tcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
                                              |  |   |  ||  | | | | ||   |  || | |||   |||   ||   || |  ||| |     || |     ||||      ||||| ||     | | |||||| |||||||||||||| || |||||||||||||||   |||||   ||| || ||||||||||||||||| ||  | ||  | |||
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG

upper sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
-------------------------------acttagaaactgca-ttcagtgatagaatg-acttgcttgaatgcttgg---catgttttttgttcacatgtcctgacgccttaaaa---cgaattttctatcat---cagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
                                 |  |   ||    ||||||   | || |  |  || | |||   ||    ||   || |  ||| |   ||   |      || |   ||| ||   | |  |   |||||| |||||||||||||| || || ||||||||||||   |||||   ||| || ||||||||||||||||||||  | ||  | |||
gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG

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|211535329|gb|FL357693.1|FL357693
EST:     GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|60350253|gb|DN217226.1|DN217226
EST:     GAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|211376353|gb|FL146646.1|FL146646
EST:     GGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|18964528|gb|BM661058.1|BM661058
EST:     GGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACCTTTCAGGTGG
genomic: GGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|18964529|gb|BM661059.1|BM661059
EST:     GGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|211376351|gb|FL146644.1|FL146644
EST:     GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|87151897|gb|DY396686.1|DY396686
EST:     GCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|211084967|gb|FL399106.1|FL399106
EST:     GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|211376352|gb|FL146645.1|FL146645
EST:     GCATATAAGATAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|211072830|gb|FL342711.1|FL342711
EST:     GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGN
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|31359162|gb|CD443519.1|CD443519
EST:     GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
EST: gi|67026048|gb|CO454797.1|CO454797
EST:     GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGG                         GAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGG

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), 47 (downstream exon)
Score: 178

GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 199

GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCCACCAACCTGGGgtatgcttct ... ctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcatgttttttgttcacatgtcctgacgccttaaaacgaattttctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
                     tcctgac  putative branch site (score: 199)
                                         ttttctatc  putative PPT
                               ttaaaacgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttagaaactgcattcagtgatagaatgacttgcttgaatgcttggcatgttttttgttcacatgtcctgacgccttaaaacgaattttctatcatcagGAGATGGGACAAATTTGAAGAATCGTACAGAGTAATGCACTTTTCAGGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA