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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagatgattctatctttttcaggagaaaatattactcatcgacagtactaacatggctagagtggatttcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAAT

Basic information

species Zea mays
transcript GRMZM2G168412_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168412_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g74190.1 (Oryza sativa), 3'ss of exon 8
--------gtatcagatgattctatctttttcaggagaa-aatatta---ctcatcgacagtactaacatggctagagtggatttcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAAT
                ||  || || |  || ||  ||| |||  ||   ||  |  ||   ||||||  | ||  | || ||| | |  |||||||||||||| || | |||||||||||| ||||| || ||||| ||||| | ||  ||||| |||||||| ||||||||||| ||||| ||||| || ||
gtatgctcactatgcctggatccatgtgcttaagaggaataatgctaaagctgctttaccaaactaacgcgcctgaactgaattccct--ccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGAT
















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|91878765|gb|EB408722.1|EB408722
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|71766718|gb|DR964655.1|DR964655
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|88747606|gb|DY531747.1|DY531747
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTTTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTT
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|13150086|gb|BG320408.1|BG320408
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAARGAGCATGCCGAA
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAA
EST: gi|13149611|gb|BG319933.1|BG319933
EST:     TTACTRCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTK-TTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|78122643|gb|DV541027.1|DV541027
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|60345957|gb|DN212930.1|DN212930
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|71328602|gb|DR800966.1|DR800966
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|78118843|gb|DV537227.1|DV537227
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|76286139|gb|DV025707.1|DV025707
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|76015835|gb|DT943005.1|DT943005
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
EST: gi|78093019|gb|DV521393.1|DV521393
EST:     TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC
genomic: TTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtatcagatg ... tcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaatattactcatcgacagtactaacatggctagagtggatttcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAAT
                      tactaac  putative branch site (score: 0)
     atattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcagatgattctatctttttcaggagaaaatattactcatcgacagtactaacatggctagagtggatttcgtggccagCTGGGATTAACGATGAAAAGGAGCATGCCGAAGAGCTAGCAGAACTACTTCGTATGTGTGGAGGTGGTTACCATGTGAACCTGATTCCCTATAACCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG