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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattatagactaacagcccaatctatatagtctaacaattctcatatgccaaaatttccctgaataaaatttaatcatataattaacttttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTGCTGCTGGTGCCGCCAAGGGCTTAGAGTACTTGCATGATAAGGCAAGTCC

Basic information

species Zea mays
transcript GRMZM2G140590_T06
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 3
taaattatagactaacagcccaatctatatagtctaacaattctcatatgccaaaatttccctgaataaaatttaatcatataattaacttttatg--ttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTGCTGCTGGTGCCGCCAAGGGCTTAGAGTACTTGCATGATAAGGCAAGTCC
  | |  ||  |  |  |     || |||     ||   | | |  | |     ||||| | ||| | | |  |    |  |  |  |||||| ||  ||||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| ||||||||||| || | ||||||||| ||||||| |||
agactcttaagcgcattgtttgttc-ataagacgtatttagttt-gtttaaattaatttgcatgattcataaatggcaacgttttgtacttttgtgtgttagATATTCCACCTGACAAGGAACCTCTCGACTGGAATACACGGATGAAGATTGCTGCTGGTGCAGCCAAGGGCTTGGAATTCTTGCATGACAAGGCAAATCC

upper sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
taaattatagactaacagcccaatctatatagtctaacaat-tctcatatgccaaa---atttccctgaataaaatttaatcatataattaact-tttatgtt-agATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTGCTGCTGGTGCCGCCAAGGGCTTAGAGTACTTGCATGATAAGGCAAGTCC
      | |   |  |     |   |  ||| | | ||| | | | ||  |  ||    | || |   |||   | || || |  | |||  ||   | | || |||| ||||||| || ||||| |||||||||||||| ||| | |||||||||||||||||||| || || || || ||||| ||||||||||| ||||| ||
------acaatttttcccaaaatcattcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactttatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
















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|32830961|gb|CD970639.1|CD970639
EST:     TCTTGTCTACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATG                         ATATTC-ACCTGATAAG-AACCTCTGGACTGGGATACACGTATGAAGATTG
genomic: TCTTGTATACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATGgtaagtttgc ... tttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG
EST: gi|71321773|gb|DR797574.1|DR797574
EST:     TCTTGTATACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATG                         ATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG
genomic: TCTTGTATACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATGgtaagtttgc ... tttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG
EST: gi|33100194|gb|CF060154.1|CF060154
EST:     TCTTGTCTACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATG                         ATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG
genomic: TCTTGTATACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATGgtaagtttgc ... tttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG
EST: gi|71432552|gb|DR813602.1|DR813602
EST:     TCTTGTATACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATG                         ATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG
genomic: TCTTGTATACGAGTTTATGCCATTGGGATCACTTGAGGATCATTTGCATGgtaagtttgc ... tttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgccaaaatttccctgaataaaatttaatcatataattaacttttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTGCTGCTGGTGCCGCCAAGGGCTTAGAGTACTTGCATGATAAGGCAAGTCC
                                     aattaac  putative branch site (score: 2)
                                           cttttat  CT-rich tract
                 tgaataaaatttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattatagactaacagcccaatctatatagtctaacaattctcatatgccaaaatttccctgaataaaatttaatcatataattaacttttatgttagATATTCCACCTGATAAGGAACCTCTGGACTGGAATACACGTATGAAGATTGCTGCTGGTGCCGCCAAGGGCTTAGAGTACTTGCATGATAAGGCAAGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT