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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatatttattattattggaccatgtggacctaaccactgagttctgaattcttctattactttgacttttggtactaatctgtaatttttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC

Basic information

species Zea mays
transcript AC195874.2_FGT002
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 3
------------------------------------------------------------aaatatttattattattggaccatgtggacctaaccactgagttctgaattcttct-attactttgacttttggtactaatctgtaatt--tttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC
                                                              || | |   || | ||  | ||| ||  ||         | ||| |  |  ||| |||   |  ||  ||| |     | ||  | |   || |  |||||||||| || |||||  | || |||||| ||||||||||  ||||||| ||||| ||||| || || ||||||||||| ||||| || || || ||||| |
gtcagtactctctccacgattttcaatttcttcctttgctttcgctgagttgtaattgcattatttctgacatgaatgttctatgaggttcttcttttgttgctcttaggttgtctcatttgctatacaattgattgccgtttgatagtaacttgtcttgcagTTTCGTACGCACAAGATAATATACAGGCGATATGCTGGGTTGTTTTTCTCAATCTGTGTTGATATCACTGATAATGAGTTGGCGTATTTAGAGTGCATCC

upper sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 3
-------aaatatttattattattggaccatgtggacctaaccactgagttctgaattcttctattactttgacttttggtactaatctgtaatttttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC
        |  |     |  | |  ||| || |  |   || || || ||    |  | | |  | |   |||  ||  |||  |   | ||||||| |||   ||||| || |||||||| || ||||||||| ||||||||||| |||| || ||| | ||||| || || ||||||||||| || ||||| ||||| ||||| |
agatttagagcagggggtcctttgtgactat-tttattaaatcattgtgtagc-agctgtccattgagcatga--ttaagtaggagatt-taattttcctt--tcagTTCCGTACACACAAGGTCATCTACAGGCGATATGCTGGATTGTTCTTCTCATTGTGTGTTGATATCACTGATAATGAGTTAGCATATTTGGAGTGCATCC

upper sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
---aaatatttattattattggaccatgtggacctaaccactgagttctgaattcttctattactttgacttttggtactaatctgtaatttttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC
     | | ||||||| | |  |   | |  || | |||  |   | |||   |||  |        | ||  |  |||     | ||| ||||  | ||||||| || |||||||| || ||||||||| ||||||||||| | ||||| ||| | ||||| || || || |||||||| |||||||| || || ||||| |
ccagcacaattattatcaatt-attttata-acattacctttacatgctgttctctattggattaagggctgattatacctgattataaatttttct-tgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC

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|60336636|gb|DN203609.1|DN203609
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|32909659|gb|CF014471.1|CF014471
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264888|gb|FL091722.1|FL091722
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264881|gb|FL091715.1|FL091715
EST:     TACACCGGCTCGTGGTCAATCAGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACT
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACT
EST: gi|211262443|gb|FL091703.1|FL091703
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|16916618|gb|BM072921.1|BM072921
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264892|gb|FL091726.1|FL091726
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|33103150|gb|CF063110.1|CF063110
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211262447|gb|FL091707.1|FL091707
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211262444|gb|FL091704.1|FL091704
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211262446|gb|FL091706.1|FL091706
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264878|gb|FL091712.1|FL091712
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|32909660|gb|CF014472.1|CF014472
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|22545654|gb|BU098013.1|BU098013
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264891|gb|FL091725.1|FL091725
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264887|gb|FL091721.1|FL091721
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|60346385|gb|DN213358.1|DN213358
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211267313|gb|FL091727.1|FL091727
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|78025572|gb|DV493959.1|DV493959
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211262445|gb|FL091705.1|FL091705
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|4827606|gb|AI668298.1|AI668298
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211264880|gb|FL091714.1|FL091714
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211262451|gb|FL091711.1|FL091711
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|211006384|gb|FL072067.1|FL072067
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTATAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA
EST: gi|71422803|gb|DR805854.1|DR805854
EST:     TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAG                         TTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGNNNNNNNCA
genomic: TACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCA

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: 386

GTACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 903

GTACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 747

GTACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 509

GTACACCGGCTCGTGGTCAATCGGGACCCTAAGTTCACCAACTTCGTCGAGgtaatcgtgt ... tcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattcttctattactttgacttttggtactaatctgtaatttttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC
                            tactaat  putative branch site (score: 509)
                                         tttttcttat  putative PPT
                               taatctgtaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatatttattattattggaccatgtggacctaaccactgagttctgaattcttctattactttgacttttggtactaatctgtaatttttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC

- - - - - - - - - - -catgtgg
- - - - - - - - - - - - - - - - - ccactga
- - - - - - - - - - - - - - - - - - - - - ttctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtact