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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttgctacctgttgtcatccactatagaaatatatctgatgacgtgtttgtttaacattaaatacattatccccttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG

Basic information

species Zea mays
transcript GRMZM2G171469_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171469_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 3'ss of exon 8
gtactttgctacctgttgtcatccactatagaaatatatctgatgacgtgtttgtttaacattaaatacattatccccttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG
      | ||| || || ||||   ||        | |  | ||    |   |  ||  ||||    |||  |||  ||||| |  ||||||| |||||||| ||||| ||||||  | ||||||||||||||||| |||||
-----gtactatcttttatcattggcttctattccagaattaatactttagataatttgcatttctaacac-atctactttttcatagGTTGGATATGTGACAACCATATGCTTTTCTGGCTTCTTGATCAGATGCGTAATG
















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|78108686|gb|DV527104.1|DV527104
EST:     GCAGCGGTTTCC-TGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAG                         GTTGGCTATGTGACCACCCTTTGCTTT
genomic: GCAGCG-TTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTT
EST: gi|91873273|gb|EB403230.1|EB403230
EST:     GCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTTGA-TGAA                         GTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCAT
genomic: GCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATT-GAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCAT
EST: gi|5895618|gb|AW036864.1|AW036864
EST:     TGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAG                         GTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATA
genomic: TGCAGCGTTTCCCTGTTGAGTCAAAAGGCCGCCGGAAAAAATTGAATGAGgtactttgct ... ttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatctgatgacgtgtttgtttaacattaaatacattatccccttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG
                    gtttaac  putative branch site (score: 3)
                                   cattatcccctttt  putative PPT
                 tttgtttaacattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttgctacctgttgtcatccactatagaaatatatctgatgacgtgtttgtttaacattaaatacattatccccttttacgcagGTTGGCTATGTGACCACCATTTGCTTTGGTTGCTTCTTGATCAGATGCATAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG