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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaatgcacctcatctctgaaagaaatacattttccctgctgctcatatttttatatactcactgttggttgggtgtataaatttaccttatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTTACAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAA

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 14
--------------------------tgtaatgcacctcatct--ctgaaagaaatacattttccc----------tgctgctcat-atttttatat--actcactgttggttggg--tgtataaatttaccttatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTTACAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAA
                          | |  |   || ||||   || |||   |  ||||   |           ||||||  || ||||||| ||  | |    ||| ||  |   ||   | | | | | | || |||||||||||||  | |||||||||||||||||    || || || |||||||||||||| |||||||||||||||||||| |||||||||||||| |||||||
gtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcagGAAGTGCTGTTGTGGATCAAATCTGTAATAGGTGAGACAGGTAGTGATGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAA

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 14
-----------------------------------------------------------------------------tgtaatgcacctcatctctgaaaga---aatacattttccctgctgctcatatttttatatactcactgttggttgggtgtataaatttaccttatat----tgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTTACAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAA
                                                                             | |   |||  | |||| || ||||   || | | | | ||| |   |  ||  || ||||  | | |||  ||  |     |||   ||  | | ||    ||||||||||| |  | |||||||||||||||||    || ||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| |||||||
gtatgctcagtttgttgtactggatcttctctgccacatcctgctaaacaaggattcactgcattgcatactcaaaatatgtcgcagattatctttggaagaaggaacataatgttccttccatttttaaattgatat-tttagtgtgtgtgtgtgaactaaccatagttcacatccaatgcagGAAGTGTTGTTGTGGATCAAATCTGTAATAGGTGAGACTGGTAGTGACGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAA
















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|6020672|gb|AW065480.1|AW065480
EST:     CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
genomic: CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     ATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
genomic: ATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
EST: gi|31361054|gb|CD445411.1|CD445411
EST:     CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
genomic: CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     CTTGCAAATCAG                         GAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
genomic: CTTGCAAATCAGgtatgctcag ... tatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
genomic: CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
EST: gi|5915419|gb|AW053060.1|AW053060
EST:     CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT
genomic: CAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttttatatactcactgttggttgggtgtataaatttaccttatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTTACAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAA
            tactcac  putative branch site (score: 1)
                                      tttacctt  putative PPT
                              tgtataaatttacctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaatgcacctcatctctgaaagaaatacattttccctgctgctcatatttttatatactcactgttggttgggtgtataaatttaccttatattgcagGAAGTGCTTCTATGGATCAAATCTGTAATTCAGGAAACTGGGAGTGATGTTACAACGGATCAACTCAAAGAGTATGTCTGGAAGACACTAAAGAGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA