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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaatgctacagttacttctgtctttgttcaatagctactgcatgcattgacgaacatctccaacaaatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG

Basic information

species Zea mays
transcript GRMZM2G098011_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaatgctacagttacttctgtctttgttcaatagctactgcatgcattgacgaacatctccaacaaatgaact---tgtactt-----tgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
                                        |  || |    ||| |   |  | ||  |    |  |||||||    ||||||  |   ||   ||||||  ||||||| ||| ||   |   |||     ||||||| ||||| |||||||| |||||| |||||||||| |||||||| |||||||||||||||||||||||||| ||| || |||||||||| ||| ||||||
---------------------------------------gttgtgataac-tgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG

upper sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 6
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaatgctacagttacttctgtctttgttcaatagctactgcatgcattgacgaacatctccaacaaatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
                                              || | | | ||  ||   |||  | ||   |  |  | ||  || |  |||  | |||     | |     || |   ||  || |  |||||| ||||||||||||||||||||  | || || || ||||||||||||||||| |||||||| ||||||   ||  || | |||||  ||||| ||||||
---------------------------------------------gtgct-ttatatattattcttatctttgagatcatagactaaataatttatg--tggac-----tgtgtggtaactc--ctcttaatgggcagATTTCACCAACTGAAATTCGTGGTGCGCTAGGATCTGTTAATCAACTTTTTATATGCATTGGGATTCTTCTGGCACTGGTGGCTGGGCTGCCTCTGGCAG

upper sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT5G16150.3 (Arabidopsis thaliana), 3'ss of exon 5
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaat--gctacagttacttctgt-ctttgttcaatagctactgcatgcattgacga---acatctccaacaaatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
                                            | ||||   | |     |    ||| || ||  ||||   ||  || |  |  ||   || |      |  ||||  |    |    |  |  ||  |||||||||||||||||||| |||||| |||| || || || || ||  | || ||||| || ||||| |||||||| ||| |||||||||| ||  | ||||
--------------------------------------------gttgtttaaatactgattttcattatttttgcacttttagcataagatgttagatttgtttatatgttatgtctctgaagcgtttgatgatggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG

upper sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 6
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaatgctacagttactt-ctgtctttgtt-caatagctactgcatgcattgacgaacatctccaaca----aatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
                                               || ||  |||| | || ||  |   | |  || ||    ||  |  ||   |  || | |||   ||   | |    ||   | ||  | |   ||||| ||||||||||||||||||||  | ||||| || || |||||||||||||| || ||||| ||||||||||| ||| | |||||||| ||| | ||  
-----------------------------------------------gtagt--aatgtttcaatttttcattattattattatgctattttttgttcgtttttatgaatgcctttgaaactgaaacacattttaaatggtcagATCTCACCAACTGAAATTCGTGGTGCGCTTGGGTCTGTCAATCAACTTTTTATTTGTATTGGGATTCTTGCAGCATTGGTGGCTGGATTACCTCTAGCCA

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|32808986|gb|CD961220.1|CD961220
EST:     GATCTCATCTGCACTTGGTACCCCTTTACATATCTGAG                         ATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTA
genomic: GATCTCATCTGCACTT-GTACCCCTTTACATATCTGAGgttgtgatac ... tactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTA
EST: gi|13198611|gb|BG354413.1|BG354413
EST:     GAATTGGTATTGGGATCTCATCTGCACTTGTACCCCTTTACATATCTGAG                         ATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTT
genomic: GAATTGGTATTGGGATCTCATCTGCACTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagctactgcatgcattgacgaacatctccaacaaatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
              cattgac  putative branch site (score: 3)
                               aacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaatgctacagttacttctgtctttgttcaatagctactgcatgcattgacgaacatctccaacaaatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA