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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactaaatagcttgttgtaaccaatgcccaactccaacataaactgcaacttgaactttctacaattcttatcataatttttccacgattcattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG

Basic information

species Zea mays
transcript GRMZM2G042027_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 8
cactaaatagcttgttgtaaccaatgcccaactccaacataaactgcaacttgaactttctacaattc------ttatcataatttttccacgattcattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG
   |  |||     |||| || | |  |  |||||| ||| ||||| ||||  || ||     ||||       |||  |  |  ||| |||  ||   | | ||||| || |||||| ||||||||||||||||||||||||| |||||||||||||
--attgataatcc-ttgtgac-attttctgactccaccatgaactgtaactgtaatttcaagaaatttatggatttactaccaccttttcac--ttgtctgttcagGCCAAGAGGGAGCTGAATGATCCAGAGAATGCACTTATTGGTGCTTTTGCTG

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 8
---cactaaatag-cttgttgtaaccaatgcccaactccaacataaactgcaacttgaactttctacaattcttatcataatttttccacgattcattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG
    |    |||  ||| ||  |   ||  |  |      |  |    |||  ||  |  |   | ||    |  | ||     || ||    |  ||  | ||||  ||||  |  ||||||||||||| |||||| |||| ||||||||||| |
atttataggataaacttattaaaggaaagacggattggtgatgt---ttgctcctctatttcatttcatgattggtgatgtgacttgcattcctttttg-ctagGCACAAAGAAATCTGAATGATCCAGAAAATGCAATTATTGGTGCTTTTGCAG

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 9
cactaaatagcttgttgtaaccaatgcccaactccaacataaactgcaacttgaactttctacaattcttatcataatttttccac----gattcattat--ccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG
    | ||   | |    |||  ||    ||    || | | | ||    |      | ||  | ||| | |||| |||  | ||      |||| || |  | ||||   |||  |  ||||||||||||| |||||| |||| ||||||||||| |
---catatttataggctaaacttat---taaaggaaagacagattggtgatgtttgctcctctatttcatttcatgattggtgcaacttaaattcctttttgctagGCACGAAGAAATCTGAATGATCCAGAAAATGCAATTATTGGTGCTTTTGCAG

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|78092776|gb|DV521150.1|DV521150
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|28984641|gb|BQ539144.2|BQ539144
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|113702185|gb|EE679689.1|EE679689
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|113702087|gb|EE679591.1|EE679591
EST:     TGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: TGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|71302081|gb|DR787128.1|DR787128
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|16918359|gb|BM073712.1|BM073712
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|91056577|gb|EB166995.1|EB166995
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|33092443|gb|CF052437.1|CF052437
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTG                         GCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT
genomic: CCATCCAGTTCTGCATTTATGAGCAACTTCGAATTGGCTACAAACTTGTGgtaccgttcc ... cattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaacttgaactttctacaattcttatcataatttttccacgattcattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG
               tacaattcttatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactaaatagcttgttgtaaccaatgcccaactccaacataaactgcaacttgaactttctacaattcttatcataatttttccacgattcattatccagGCGAAAAGGGAGTTGAATGATCCAGAGAATGCACTTATCGGTGCTTTTGCTG

- - - - - - tgttgta
- - - - - - - - - - -caatgcc
- - - - - - - - - - - - - - - - - caacata
- - - - - - - - - - - - - - - - - - - - - -ctgcaac