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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagggctataactataactgcacaaaagcctgcctttcgaagcatataggaggcttctaatttattcctcttattgaccttttctgttcacctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGATTCTGAGCAGTACAACAAACTTGAGAGACCCGTACGTGATGAATGTGAA

Basic information

species Zea mays
transcript GRMZM2G055520_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055520_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g06070.1 (Oryza sativa), 3'ss of exon 6
-tgagggctataac-tataactgcacaaaa-gcctgcctttcgaagcatataggaggcttctaatttattcctcttattgacctt----ttctgttcacctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGATTCTGAGCAGTACAACAAACTTGAGAGACCCGTACGTGATGAATGTGAA
 |   |  | |||  ||| |||| |||||| |  ||||||  | | |  |||  ||  ||  | |||| |  |  |||||   |     || |||| | ||    ||||| || || | |||||||||||||||||||||||| ||||| ||||| ||||| |||||||||||||| || |||||| | |  ||||||||||| |||
ttttcgtttctaaggtatcactgaacaaaatgtttgcctt--ggatcg-ataaaagtgttacattttaat--tgatattgggttcacaattttgttgatctt--tagGTATGATGATCAGTTTGTTATGGTGAATTTTGATGGAGATCCTACTGCCGATTCAGAGCAGTACAACAAGCTAGAGAGATCTGAGCGTGATGAATGCGAA
















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|67028367|gb|CO457116.1|CO457116
EST:     GTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTG-TTTCCGATAG                         GTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTG
genomic: GTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTT-TGATAGgtatttactt ... acctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTG
EST: gi|6445442|gb|AW179360.1|AW179360
EST:     CTTTGCTACCTGATTTTGATAG                         GTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
genomic: CTTTGCTACCTGATTTTGATAGgtatttactt ... acctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
EST: gi|51592768|gb|CV071914.1|CV071914
EST:     CGTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTTTGATAG                         GTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
genomic: CGTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTTTGATAGgtatttactt ... acctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
EST: gi|6445422|gb|AW179490.1|AW179490
EST:     CTTTGCTACCTGATTTTGATAG                         GTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
genomic: CTTTGCTACCTGATTTTGATAGgtatttactt ... acctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
EST: gi|76286686|gb|DV026254.1|DV026254
EST:     CGTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTTTGATAG                         GTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
genomic: CGTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTTTGATAGgtatttactt ... acctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
EST: gi|101389744|gb|EB816806.1|EB816806
EST:     CGTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTTTGATAG                         GTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA
genomic: CGTGGGATGCAAGCTGAGTGGGTTATGCCTTTGCTACCTGATTTTGATAGgtatttactt ... acctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataggaggcttctaatttattcctcttattgaccttttctgttcacctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGATTCTGAGCAGTACAACAAACTTGAGAGACCCGTACGTGATGAATGTGAA
                           tattgac  putative branch site (score: 2)
                                 ccttttctgttcacct  CT-rich tract
          ttctaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagggctataactataactgcacaaaagcctgcctttcgaagcatataggaggcttctaatttattcctcttattgaccttttctgttcacctaaacagGTACGAGGAGCCGTTTGTTATGGTGAATTTTGATGGCGATCCAACTGCTGATTCTGAGCAGTACAACAAACTTGAGAGACCCGTACGTGATGAATGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - -actgcac
- - - - - - - - - - - - - - gcctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - ggcttct