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

gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG

Basic information

species Zea mays
transcript GRMZM2G093643_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 10
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaatt--ttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                                  |    |||  ||     ||   |  | | | | | | | |||   |  |  |  |||||    |||| ||  || || || |  | | |||| | |  |||||||||| || || |||||||| |||||||||||||||  ||| ||||||||||||||||||||||| ||||||||||||||||| ||||||||||| ||||
-------------------------------------------------------------------------------------------------actgcacatttatagcccttgttgcctgtgtgctcattctgctctctagaatttgattat----aactgttcgatttgtaagttatcctttttatgttgaacagTTGCTTCGTCCAATTTACAAGCAAATTGCTGAAAATAGGAACGCTGAGATATTTTCAGCAAATACTCTCCTTGTTATTTTTGGAACAAGTCTTCTCACAG

upper sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 17
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                              | |   |   ||   |    | |||| |||      | |||||  ||| |  ||  ||  | |  |  |   |||    ||   |||  ||| |   |   |||| | || || || || ||||| ||  |||| |||||||| ||||| || || || ||||| |||||||||||||||||| |||||||||||||||||||||
----------------------------------------------------------------------------------------------gataagtgatatcattttggggttca-tttggaaggcattgca--tgcttcaattgcagatgtagagtatgctttgtgctgagttttctgttcttcttt--acagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCTAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 13
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctaca---actatttaatgtgc-aattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                                    |   ||   |    | ||||  ||      | |||||  ||   |||  ||||||    |     | |||    |||||  | |||| | || |     |||| | || || || || ||||| ||  |||| |||||||| ||||| || || || ||||| |||||||||||||||||| |||||||||||||||||||||
----------------------------------------------------------------------------------------------------tgatatcattttggggttca-cttggaaggcattgca--tggtggtacttcaattgcagatgtagagtatgctttgtgctgagtttcctgttcttctttacagCTCCTTCGACCAATATACAAGCAGGTTGCAGAAAATCAAAATGCAGAAATTTTCTCAGCCAATACACTCCTTGTTATTCTTGGCACAAGTCTTCTTACAG

upper sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                            | ||||   |||||  |   ||  |  |  | | |  |   |||   ||| | |       | |   | |  | |  ||||      |||  | | ||| || |||| | || ||||| || ||||| |||||||| ||||| |  |||||||||||||| || || |||||||| || |||||| |||| || ||| | |||||||
------------------------------------------------------------------------------------------aatgggtt---tgcatgaacatataatgaaactctatagctaatgc---tgcttctgcggtgctgaatcatagttttacaatgcattgattt--tctggta-cacacagCTTCTGCGGCCGATATACAAGCAAATTGCAGAAAACCGAAATGCTGAGATATTCTCCGCCAATACACTTCTGGTTATTCTTGGGACTAGTTTACTTACAG

upper sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 8
gtgagttgactgttcatttacattattttgcttatcctttctggtactttttgtatgccatacgtagactctgggcccagctggacataggtttggttccttgcatacatgcatgtttcagtttttttccccttgcagctgcatgtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaa-----acagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                                                                                                          | |    |||| |||  | |      || |  || ||  ||| |  || |  |||| |  |  |   |||| || |  ||||| |||        ||| | ||  | || ||||| || ||||||||||||||||| ||||| ||||||||||| || |||||||| |||||||| || || || ||||| |||||||
------------------------------------------------------------------------------------------------------attgagacttgtgttacagcatctgatatgtttctccttcagttat-tatatgaagtacagcc-tgcaccttgcacttatttttttgcatctgcttttgcagCTACTTAGACCAATTTATAAGCAAATTGCTGAAAATCAAAATGCAGAGATATTTTCTGCCAATACACTTCTTGTTATCTTGGGGACTAGTCTCCTTACAG

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|78103566|gb|DV521994.1|DV521994
EST:     CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG                         TTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATA
genomic: CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagttgac ... tatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATA
EST: gi|71325401|gb|DR799380.1|DR799380
EST:     CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTG                         TTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATA
genomic: CAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagttgac ... tatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATA

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), 45 (downstream exon)
Score: 87

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagttgac ... tatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagttgac ... tatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 32

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagttgac ... tatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 72

GTTGGTTTCCAAGCAATAGCAGAAGCCATGGGAATGGCTGCAGTCAAAGCAGTAGCTGCTATAACTGCCATAATTGCTGGAGGTCGTCTGgtgagttgac ... tatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctcaattatctacaactatttaatgtgcaattttcgttttgtatcaaacagTTGCTCCGGCCTATTTACAAACAAATTGCTGAAAATCAGAATGCTGAGATATTTTCAGCAAATACACTCCTTGTTATTTTTGGCACAAGTCTTCTTACAG
                     atttaat  putative branch site (score: 72)
       aattatctacaactat  TA-rich tract