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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcatggagtccccctttaacattgcattaggctctttttaaatgctctgcgcttctgcttacgtggcactgagacacctcatctttattacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG

Basic information

species Zea mays
transcript GRMZM2G017089_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 15
aactcatggagtccccctttaacattgcattaggctct---ttttaaatgctctgcgcttctgcttacgtggcactgagacacctcatct-ttattacgtt-cagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG
 |   |||   |  |       | |||| |   | | |   || |||| |  |      |  | | |  |   ||| | ||   ||| |  || | || || |||||| ||||||||||| || || || ||||||||||||||||| ||||||||||||||||||||||
-agcaatgtgatttcaag--ggctttgcttactgttgtaacttgtaaacgaacaatagctaggatcatata--acttaaacttgtcaccgattgtcacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGTCTTGGCAACTGGAG

upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 14
----aactcatggagtccccctttaacattgcatta--ggctctttttaaat--gctctg-cgcttctgcttacgtg------gcactgagacacc--tcatctttatt-acgttcagGT-CGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG
      |||    ||       |  || ||||||     |  ||||| ||||  |  ||| |  |  |  ||| ||       |   |   |||    | |||||| |  | |   | || |||| |||||||| ||||| ||| ||||||||||||| |||||||||||  |||  |||||||
gtaagtctctgctagataattatatactttgcatctccagtgcttttgaaataggagctgtcattattaattatgtaattgatgtgtttgaacaatgtttatctttttccatggaaaagTTCGCAACAGAAAACCATAATTAATGCAATGGCTGTAAACGAGGATGGTGTGATGGTCACTGGAG
















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|60342895|gb|DN209868.1|DN209868
EST:     CCAAAGGCGAATTTATGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: CCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|31909551|gb|CD650975.1|CD650975
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33091976|gb|CF051970.1|CF051970
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|37376961|gb|CF625047.1|CF625047
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|76013075|gb|DT940245.1|DT940245
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|4967045|gb|AI691809.1|AI691809
EST:     GTAAA-AAGTTTAACCTTCCCAAAGGCGAATTTCTGCNCANCATGCT                         GTCGCAGCAGAAACCAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: GTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|6538870|gb|AW225009.1|AW225009
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTTTGCCCAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|31406178|gb|CD484910.1|CD484910
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|71416740|gb|DR803804.1|DR803804
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33091991|gb|CF051985.1|CF051985
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33093989|gb|CF053983.1|CF053983
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|5055899|gb|AI734786.1|AI734786
EST:     AAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCNCAACATGCT                         GTCGCAGCAGAAACCAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|37382890|gb|CF628417.1|CF628417
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCG-ATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|101383542|gb|EB813827.1|EB813827
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|32933315|gb|CF038127.1|CF038127
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctgcgcttctgcttacgtggcactgagacacctcatctttattacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG
             tgcttac  putative branch site (score: 2)
                                       tctttatt  putative PPT
                                      atctttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactcatggagtccccctttaacattgcattaggctctttttaaatgctctgcgcttctgcttacgtggcactgagacacctcatctttattacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG