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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT

Basic information

species Zea mays
transcript GRMZM2G138410_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 2
gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgta-aatgcatctgcacctggtacttatttatatgcatgctacgc-tgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
||||| |  |||  || ||    | ||| ||||| || ||   |  |||  | ||  ||  ||  |     |  | || |  ||    |||| |      |  ||| || || | |   |    | || || ||||||||||||||  ||||||||||||| ||||||||||| || |||||||| || ||||| ||||||||||||||||||||||||| ||| ||||||| |
gtaaaacacgctataaaat----agtat-tatctttttattcctttttacttcttttatacttttcaaaagcagcaatttgtaacatctctgtaaagtaaaagtatctaaattcctaaaatatgtcttttctagATTTGATGCTGTCGTTCATTTTGCTGGTCTGAAAGCTGTGGGTGAAAGTGTGCAGAAGCCATTGCTTTATTATGACCATAATGTTGCTGGGACAATAATT

upper sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
--------------------------------gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtt--tagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
                                 | |  ||   | ||  || | ||  |  ||| |    || |||||   |   ||  ||||   |     |||  ||| |||| || |||  || | ||  |||| ||   |       |    | |  | |||||| |||||||| || |||||||||||||||||||| || ||||||||||| ||||| ||||| || || ||| || | ||  |   ||| ||||| | |
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtat-gacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacat-cattagc-cttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT

upper sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
-----------------------------------------gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagcct-tgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
                                          | |  ||   | ||  ||     |  | | | |  | || |||||  ||  ||| |    |  |    | | |||| | |  |      ||  | ||  |||| ||   |    |  | |  | |  | ||||||||||||||| || || ||||||||||||||||| || ||||||||||| ||||| ||||| || || ||| || | ||  |   ||| ||||| | |
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaat-attattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttt-tcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT

upper sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
|||    |      || |    || | | |     |    | || || |   |  |||||  |     ||  |  ||| |   |  ||       || |  | ||  |  || |        | || | ||| |||||||| || || |||||||||||||| ||||| ||||| || |||||| | |||||||||||||||||| |  ||||| ||||||| || || | |
gtatgattgagaaaaaaacaaacattcttttagcttcttcactttatcactaa--caatgagtgataatgcatattat-tgggtttattctttattgat--tgatgaacgtggaattattattattttacagGTTTGATGCAGTGATACATTTTGCTGGACTTAAAGCAGTTGGTGAGAGTGTAGAGAAGCCTTTGCTTTATTATAATAATAATCTTGTTGGTACTATTACT

upper sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
                          | | |    |  | |||  |||   | ||  | ||  |   ||||      ||   |    | ||    |   ||||| || | | ||   |    |   || ||| ||||||||||| ||||| ||||||||  |||| || ||||| |||||||| ||||| || |||||||| | |||  | ||  || |||||||||| | |
--------------------------acagac---tgaagaatagatttgatgttacacgtagaaatttgtgcatcttgctcaactttatgt-tttataacttactt-tgtccaccttgt-ttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT

upper sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctc----cagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
                                   |  | |||  |||   | ||  ||||  |   || |  |   ||   |    | ||    |   |||  ||  ||      | ||  ||||  |    ||| ||||||||||| ||||| ||||||||  |||| || ||||| |||||||| ||||| || |||||||| |||||  | ||  || |||||||||| | |
-----------------------------------tgaagaatagatttgatgttacatgtagaaatttatgcttcttgctcaactttatgt-tttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT

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|148994391|gb|EE034074.2|EE034074
EST:     GTTGATATCCGTGACAAAGATGGATTGGAAAAGGTTTTTGCTTCAACAAG                         ATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGT
genomic: GTTGATATCCGTGACAAAGATGGATTGGAAAAGGTTTTTGCTTCAACAAGgtaaagcttg ... tgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGT




















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: 39

GTTGATATCCGTGACAAAGATGGATTGGAAAAGGTTTTTGCTTCAACAAGgtaaagcttg ... tgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 6

GTTGATATCCGTGACAAAGATGGATTGGAAAAGGTTTTTGCTTCAACAAGgtaaagcttg ... tgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 19

GTTGATATCCGTGACAAAGATGGATTGGAAAAGGTTTTTGCTTCAACAAGgtaaagcttg ... tgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GTTGATATCCGTGACAAAGATGGATTGGAAAAGGTTTTTGCTTCAACAAGgtaaagcttg ... tgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
                                            ctgttctcc  CT-rich tract
                     tacttatttatat  TA-rich tract