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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA

Basic information

species Zea mays
transcript GRMZM2G048277_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtc-ctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
   |  || |            | | || |||   || | |  ||  || |      |        | |  || |    | ||||||  |||  | | |||||||||||||| |||| |||||||| |||||||||||||||||||| ||||||||||||||||| ||| || | || |||||||| || |||||||| ||
-tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 2
--aaattgagttgc--aactaacgtcactcttgtgtctatgcttagcttttt----ggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctg-cagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
  |||   | || |  | | |  |  ||  ||||  | ||| |||| | |||     |||     || |   |   |||  | |  |||||   |  |    ||  ||||||||||  |  | |||||||| || || |||||||||||||| || |||||| |||||||||| |||||    ||||| ||||| || || || |||||
gtaaaaaaatttccccatccacggataccattgtaaccatgattagttcttttcatagtttgtcttagaatgacattgacatctt-ttatggctttttattcctttcagCTAGGCATATCCTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGA

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatc-tgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
       || | || |  |  | |   |||  | ||| |||  | |||  |   |  |      |   |||  |||  || ||   |  |    | | |||| |||||  | || |||||||| || || |||||||||||||| || |||||| |||||||||| |||||    || || || || || || || |||||
-------gtagaaaatttc-ccccatctgtaaccatgattaattcttt--tcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------aaattgagttgcaa-ctaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
                                                 |||   | | | || | ||  |   ||       | |  |     |||||  |   |||| |  |    | |  |   ||       |  |     | |||| || || || ||||| |||||||| || |||||||| || || || || |||||||||||||| ||| |||  || || ||||| ||||||||||||||
gtgtgttttttggattcgtttctgtgcctgttacctttgttcatgagtaaaaaatactggtaaacaaatatggatccaaaagttctcttacaacttttg--tattagtacaatagcattaaagtcaaatctccaattgtttttgtttcagCAAGACATGTTTTGTGCGAGAAGCAAGGAAAGATCAACGAGGCCTACAAAAAGTTGCAGGATGGTTGGTTGAGCAACGGAGACAAGGTTCCTCCTGCTGA

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|6672235|gb|AW282401.1|AW282401
EST:     TCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: TCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
EST: gi|33096749|gb|CF056725.1|CF056725
EST:     TCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: TCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
EST: gi|18179379|gb|BM380589.1|BM380589
EST:     CAAGGGCGGCAAGTCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: CAAGGGCGGCAAGTCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
EST: gi|211107276|gb|FL481516.1|FL481516
EST:     GACTCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: GACTCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
EST: gi|9731760|gb|BE510512.1|BE510512
EST:     CAAGGGCGGCAAGCCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: CAAGGGCGGCAAGTCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
EST: gi|60355788|gb|DN222761.1|DN222761
EST:     CAAGGGCGGCAAGTCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: CAAGGGCGGCAAGTCCGCTGACGGACTCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
EST: gi|5108029|gb|AI739742.1|AI739742
EST:     TGACGGACTCGGCACTTGCACCTACGTCAAAG                         CTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA
genomic: TGACGGACTCGGCACTTGCACCTACGTCAAAGgtaccgttcc ... gcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
                    agctgat  putative branch site (score: 4)
                         atttatgattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA