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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacacgatttgccgcggatagccttaaggatttgatcagatattttccttacaacaccaacttaggcaaacatatctttatttttaccctcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG

Basic information

species Zea mays
transcript GRMZM2G069765_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 5
ttacacgatttgccgcggatagccttaaggatttgatcagatattttcctt--acaacaccaacttaggcaaacatatctttatttttacc-ctcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG
 ||  | ||     |  | |   |     |||          |  ||  ||  |    | ||  ||   |  |   |   | | ||| |    | || | ||||||| |||||||| ||||||||| | |||||||| || ||| ||||||| |||||||||||||||||||
ata-gcaataacttgtaggtgctccatcagatcaatgtgagcaactttgttggattttatcattttcttctgatgcac--taactttaattattattttttagCTGGTGAGATGCTCCATGTTGCAGAAGCATTCATTGATAAGCACTACCACCCAACTGTTATTTGCCGAG
















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|149105498|gb|EE291023.2|EE291023
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|60358233|gb|DN225206.1|DN225206
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211229383|gb|FL136771.1|FL136771
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|149082543|gb|EE171738.2|EE171738
EST:     TACACGGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTA
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTA
EST: gi|211229393|gb|FL136781.1|FL136781
EST:     ACACGGGATGAAGAAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTC
genomic: ACACAGGATGAAGAA-GTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTC
EST: gi|211227330|gb|FL136768.1|FL136768
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211231448|gb|FL136784.1|FL136784
EST:     TACACGGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATG
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATG
EST: gi|211231450|gb|FL136786.1|FL136786
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|33097192|gb|CF057152.1|CF057152
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGACGCTACATGTTGCACAGGCATTCATCG
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCG
EST: gi|76014861|gb|DT942031.1|DT942031
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211229381|gb|FL136769.1|FL136769
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|22491088|gb|BU051011.1|BU051011
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|19350690|gb|BM895222.1|BM895222
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211229385|gb|FL136773.1|FL136773
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211231451|gb|FL136787.1|FL136787
EST:     CACAGGATGAANGAAAGT-GGTGATGGCACTACATCTGTCATTGGTCTAG                         CTGGAGAGATGCTACATGGTGCACAGGCATTCATCGAC
genomic: CACAGGATGAA-GAA-GTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGAC
EST: gi|32865501|gb|CF005183.1|CF005183
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACC
EST: gi|19351773|gb|BM896305.1|BM896305
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211229388|gb|FL136776.1|FL136776
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211229394|gb|FL136782.1|FL136782
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|87153647|gb|DY398436.1|DY398436
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|31354825|gb|CD439182.1|CD439182
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|211229386|gb|FL136774.1|FL136774
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|31354522|gb|CD438879.1|CD438879
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|148949761|gb|EC895244.2|EC895244
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|31354218|gb|CD438575.1|CD438575
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|22491149|gb|BU051072.1|BU051072
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
EST: gi|149084479|gb|EE173941.2|EE173941
EST:     TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGCCATTGTTCTAG                         CTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC
genomic: TACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggtat ... tcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttacaacaccaacttaggcaaacatatctttatttttaccctcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG
 tccttac  putative branch site (score: 2)
                              tctttatttttaccct  putative PPT
                       aaacatatctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacacgatttgccgcggatagccttaaggatttgatcagatattttccttacaacaccaacttaggcaaacatatctttatttttaccctcttatctagCTGGAGAGATGCTACATGTTGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC