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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgatacgttgacatgacagttgctttgttcaaaacctaatgctgttgtgatatgtacttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG

Basic information

species Zea mays
transcript GRMZM2G153704_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
gttgtgatacgttgacatgacagttgctttgttcaaaacctaatgctgttgtgatatgtacttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtact-----ctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG
             |   ||| |  || |   ||||||   |     || |     |  |||| ||| ||  |||  ||||||| |||||||| |||  |   |   ||     |||||||| ||||| |||||||| |||||| |||||||| | |||||||| |||||||| ||||||||||||||||| ||| || |||||||||| ||||||||||
-------------gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG

upper sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 6
gttgtgatacgttgacatgacagttgctttgttcaaaacctaatgctgttgtgatatgtacttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG
                              || |   |  || |  | || |  |    |     | ||   |  ||  |  |   |        || | |   || |  |||||| ||||||||||||||||||||  | || ||  | ||||||||||||||||| |||||||| ||||||   ||  || | |||||  ||||||||||||
------------------------------gtgctttatatattattcttatctttgagatcatagactaaat-aatttatgtggactgtgtggtaactcctcttaatgggcagATTTCACCAACTGAAATTCGTGGTGCGCTAGGATCTGTTAATCAACTTTTTATATGCATTGGGATTCTTCTGGCACTGGTGGCTGGGCTGCCTCTGGCAG

upper sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 6
gttgtgatacgttgacatgacagttgctttgttcaaaacctaatgctgttgtgatatgtacttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtactctg-cagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG
             |   | |   ||   || ||||     || |  | || || |||    || ||   || || |||||   |    | |    ||     | ||    | ||||||||||||||||||||||||||  | |||||  | || ||||||||||||||||| ||||| ||||||||||| ||| | |||||||| ||||| ||  
-------------gtagtaatgtttcaatttttca----ttattattattatgctat---tttttgttcgtttttatgaatgcctttgaaactgaaacacattttaaatggtcagATCTCACCAACTGAAATTCGTGGTGCGCTTGGGTCTGTCAATCAACTTTTTATTTGTATTGGGATTCTTGCAGCATTGGTGGCTGGATTACCTCTAGCCA

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|78078828|gb|DV507240.1|DV507240
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|148996907|gb|EE035711.2|EE035711
EST:     AATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTTAC-TATCTGAG                         ATCTCACCAACTGAAATTCGTGCAACACTTGGTACCGTTAATCAACTTTTT
genomic: AATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTT-ACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|31355588|gb|CD439945.1|CD439945
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|211050167|gb|FL124868.1|FL124868
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGT-GAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|78075828|gb|DV504262.1|DV504262
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|148981335|gb|EE027589.2|EE027589
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|32847646|gb|CD987327.1|CD987327
EST:     ACCCCTTTACATATCTGAG                         ATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTT
genomic: ACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|149083192|gb|EE172463.2|EE172463
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|31355150|gb|CD439507.1|CD439507
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCCACTGAAATTCGTGGAACACTTGGTAC
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTAC
EST: gi|149082633|gb|EE171834.2|EE171834
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
EST: gi|148953947|gb|EC899333.2|EC899333
EST:     GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAG                         ATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT
genomic: GAATTGGTATCGGGGTCTCATCTGCTCTTGTACCCCTTTACATATCTGAGgttgtgatac ... tactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG
           tgttgat  putative branch site (score: 4)
                                      tttcctgt  putative PPT
                               aaatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgatacgttgacatgacagttgctttgttcaaaacctaatgctgttgtgatatgtacttctgcctgtgttgatgaacatccccaacaaatgaatttcctgtactctgcagATCTCACCAACTGAAATTCGTGGAACACTTGGTACCGTTAATCAACTTTTTATTTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTCTGGCAG

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