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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagatgcttgcggcctgtatctgcagcatcgttttctctgtctaatgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG

Basic information

species Zea mays
transcript GRMZM2G171745_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
gcaagatgcttgcggcctgtatctgcagcatc---gttttctctgtctaa-tgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG
|  |||||||||   | |  |  | ||   |    | ||||  ||| ||  ||  || |  |      | ||| | |||| | |      |||||||||||||| ||||||| |||||||||||||||||||| || || |||||||| || || ||||| ||
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
















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|166678942|gb|EG225373.1|EG225373
EST:     GGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACA
genomic: GGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACA
EST: gi|76012366|gb|DT939536.1|DT939536
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|149027222|gb|EE046433.2|EE046433
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|60398630|gb|DN231446.1|DN231446
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|78109059|gb|DV527476.1|DV527476
EST:     CGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: CGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|113702753|gb|EE680257.1|EE680257
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|211477594|gb|FL101253.1|FL101253
EST:     ATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: ATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctctgtctaatgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG
              tgataac  putative branch site (score: 2)
                                  ttttctctgcattc  putative PPT
           taatgataactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagatgcttgcggcctgtatctgcagcatcgttttctctgtctaatgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC