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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgctgaccatgaactgtaaagtttatcatggctccattactcagtggtatatcgatgttttctatagcataatttgtcacctgctttaacgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAAGGTTTGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCC

Basic information

species Zea mays
transcript GRMZM2G120302_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 16
gtatttgctgaccatgaactgtaaagtttatcatggctccattactcagtggtatatcgatgtt-ttctatagcataatt--tgtcacctgctttaa--cgttttc----tagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAAGGTTTGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCC
           | |||| ||   ||  | || ||  | | |  | | | ||||  ||   ||    | || ||   ||    | ||| |||||| ||  | |||||     |||| || ||||||||||||||||||||||||||||  ||||| ||||||||||||||||||||||| ||||| ||||| ||||||||||||||||| ||||
----------cctatgagctcataa--tcatgataac-cgagaaattaatggtgcataattgcaactgtaaagtgcaaacaatttcatctgcttcaattcattttcattccagGTAGTCCCACCAGATCAGGCACGCAAAATATACAAGGCCTTAAAAGAGAAAGGTTTGCCTGTTGCCTTGGTGGAATACGAAGGAGAGCAGCATGGTTTCC

upper sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 16
gtatttgctgaccatga-actgtaaagtt----tatcatg--gctccattactcagtggtatatcgatgttttctatagcataatttgtcacctgc-tttaacgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAAGGTTTGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCC
    ||  | || |||  | | | |  ||    || |||   |     ||| ||     | |||  ||  | |  | |    |  ||| ||  |   ||    |  ||  ||||||||||||| ||||| || || |||||||||   ||  ||||||| |||||| |||| |||||| | ||||| ||||||||||| || || || ||||
---gttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
















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|33091583|gb|CF051577.1|CF051577
EST:     TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG                         GTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
genomic: TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAGgtatttgctg ... cgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
EST: gi|5847476|gb|AW000555.1|AW000555
EST:     TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG                         GTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
genomic: TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAGgtatttgctg ... cgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
EST: gi|32935186|gb|CF039998.1|CF039998
EST:     TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG                         GTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
genomic: TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAGgtatttgctg ... cgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
EST: gi|32934798|gb|CF039610.1|CF039610
EST:     TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG                         GTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
genomic: TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAGgtatttgctg ... cgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
EST: gi|148961815|gb|EE012596.2|EE012596
EST:     TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG                         GTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
genomic: TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAGgtatttgctg ... cgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
EST: gi|148972938|gb|EE023964.2|EE023964
EST:     TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAG                         GTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA
genomic: TCAACCAGTTTACTTGTCCAGTCATTTTGTTTCAAGGGTTGGAGGATAAGgtatttgctg ... cgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatatcgatgttttctatagcataatttgtcacctgctttaacgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAAGGTTTGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCC
                                       ctttaac  putative branch site (score: 3)
                                             cgttttct  CT-rich tract
             ttttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgctgaccatgaactgtaaagtttatcatggctccattactcagtggtatatcgatgttttctatagcataatttgtcacctgctttaacgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAAGGTTTGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG