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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgtttgtcttcagttccatgctttgtgtcatctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 4
gtaaattgtttgtcttcagttccatgctttgtgtcatctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaaca-----ggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
       ||   ||||||   || | |      | |  |||      |  |   |   || |||| |||    ||||| |||||       ||  || ||||||  |  |||| |  ||  ||| ||||||       | || || |  |   ||| ||||| |  ||| |||| ||||||||||| |||||||||||||||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||
-------gtaaatcttcaaagccttccaccacctgaaatcttgtgccatgtcc-tatgtaggttttttttttgtttcaaattttg------ttttgtcttggaagttgttttttggccatagtatctaacatatgtatcgaatttgttttcaatttctcagTTTCGGTGCAGCTATACTCTCCAGACCGTCCTCTGGTTGATACTGCAGAGGTGTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G01100.2 (Glycine max), 3'ss of exon 4
----------------gtaaattgtttgtcttcagttccatgctttgtgtcatctctgtgaatacatgggtgcctatgttt--gtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
                 | |  ||| | |  |  ||   ||   || ||   | ||| |    ||| |      ||  |||     | ||   | |||||||   ||   || | |   |   |||| || |   |       ||     |   |   || ||  | |  | ||| | | |  || | |||||||||   |||||  ||||||||  ||| || |||||| ||||||||||||| |||||||||||| |   ||| || || ||
gtatgattgactttctatgagctgtctcttgtt-gtgtaattaattatggtttttcttttggcacaggacaatttaatttttaaaatgacagcttatattttatatatgatgtgaacatgtgccttacttgatatcggttgcacttctgcgtgtacaatttctgctct--ttagTGTCAATCCAGTTATACTCTCCACTGCGTCCATTGGTTGATGTTGCGGAAGTGTTTTTGTGGCTTATGGCTGTTGGTACCATTTTAATTGCTTCTTATTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 4
----------------gtaaattgtttgtcttcagttccatgctttgtgtcatctctgtgaatacatgggtgcctatgttt--gtttaacttttcatatttttggtaacttgagtattggaaacttattt--tagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
                   | |||| | |  | | |   ||   ||  | | | ||| |    ||| |   |  ||  |||     |||    | |||||||        || | |   |   |||| ||  || ||   |     |  || |   | ||     | |||    ||| |   |  || | |||||||||   |||||  ||||||||  ||| || |||||||||||||||||||| |||||||||||| |   ||| || || ||
gtatgattgactttctccgagttgtctcttgtta-tgtaattagttacggcttttcttttggcacaggacagtttaatttttaaaataaaggcttatattttatacctgatgtggacatgtgtcttacttgatattggttgcacttttgcatgtacaattcctgctcttt----agTGTCCATCCAGTTATACTCTCCATTGCGTCCATTGGTTGATGTTGCGGAAGTGTTTCTGTGGCTTATGGCTGTTGGTACCATTTTAATTGCTTCTTATTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 4
gtaaattgtttgtcttcagttccatgctttgtgtc-atctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
      | | | ||   |  ||  ||  | ||||| || | | ||     |    || || |  ||  | | |     | ||||    |||||    |||       || |||   |      |   |      ||   | | | |    |    ||| |  ||| || |||| ||||||   |||||  ||||||||  |||||| |||||| | ||||||||||| || ||||||||||| ||||| || |||| 
----ggtatgtttcactatctctgtgaat-gtgtctatttttttgtgattagtcatggctttcatttgtcagc----aaaatttggaataactactttatattttgattctttgtataattattctttgcttttctgtatgtacgtccactctcaaGTGTCGGTGCAGTTGTATTCTCCACTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTCGGTACCATTCTCTGTGCTTCTTACT-

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 4
gtaaattgtttgtcttcagttccatgctttgtgtcatctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
||| ||  ||    |||  |   |   | | | |  ||| |    ||   |  | || |   |||||   |      | ||||    |||||    |||       || |||   ||     |   |      ||   | |   |    |    ||| |  ||| || |||| ||||||   |||||  ||||||||  |||||| |||||| | ||||||||||| |||||||||||||| ||||| || |||||
gtatat--ttcactttctctgtgaatatgtatctattcttttgtgattagtatg-gctttcatttgtcacagc---aaaatttgaaataactactttatattttgattctttatatgattattctttgcatttctgcatgtatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG

upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 4
------------gtaaattgtttgtcttca--gttccatgc---tttgtgtcatctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
             ||   ||  ||  ||||  ||| ||      |||     || |   | ||| ||    ||| | ||||  |  ||   ||    |  ||||||| |     ||     |   |   || |    |  | ||   |   ||  |  | |  | ||  |||||    ||  |||| ||||||||| | ||||| || ||||| |  || ||||||||| ||||||| ||||| |||||||||||| | | |||||| |||||
gtatgctttcccttattctgcatgctttcaaggtttcaaaaatatttcaaatattttctttaattcaccattgctt-tgttgttcaaatagtttccttgattggtaaatacctgatctagcatgcaaactattttctgtaaactgttaa-ttatatggttccctattcttcagTTGCTGTTCAGCTATACTCTCCAAAGCGTCCACTTGTTGACATAGCTGAGGTGTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTG

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|149049844|gb|EE048531.2|EE048531
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
EST: gi|89758526|gb|DY687677.1|DY687677
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
EST: gi|211335511|gb|FL455439.1|FL455439
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
EST: gi|211297692|gb|FL447045.1|FL447045
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
EST: gi|148956514|gb|EC902353.2|EC902353
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
EST: gi|149081128|gb|EE170234.2|EE170234
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
EST: gi|71422117|gb|DR805619.1|DR805619
EST:     GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAG                         TCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG
genomic: GCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGG

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: 136

TGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

TGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

TGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

TGTGAGACCAATGAAACAAATTTAGATATTGGCATACATGCTGTTCTTCTGCCAAAAGATGCAGGCTCTTCTTTACAAAGGTCTCTCTCTAGTGGTGAAGgtaaattgtt ... tttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
                      agctaac  putative branch site (score: 138)
                                     ttttcctttttttgtc  putative PPT
     ttattttagt  TA-rich tract