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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaaataaagcctgtctcacgaataggcactagctagtccttctggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGGCTGCTCCAATGGGAGTTT

Basic information

species Zea mays
transcript GRMZM2G107491_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
----------tacaaataaagcctgtctcacgaataggcactagctagtccttctggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGGCTGCTCCAATGGGAGTTT
| || ||| | | | ||| | | | | | || | | | |||||| |||| | | || || |||| | |||| |||| |||||||| ||||| ||||||||||| ||||||||||||||||||||||| || || |||||||| ||||| || |||||| ||||||||||||| |
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctata--acacct-----aatgattgactat---gacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGGCTCCTCCAATGGGAGTGT

upper sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
tacaaataaagcctgtctcacgaataggcactagctagtccttctggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGG-CTGCTCCAATGGGAGTTT
| | || || | || | | | || |||||| |||| || | ||| | | | | |||| ||| ||| ||| ||||||||||| ||||| ||||||||||| || | | ||||||||||||||| || | | || | | | |
------------gtaagctaataaaagacttcagattctttcctttata-gtctcattatgtggtttggta----aattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-

upper sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
------tacaaataaagcctgtctcacgaataggc-actagctagtccttctggtaca-cctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGG-CTGCTCCAATGGGAGTTT
| | ||| | | |||| ||| | || ||| || | |||||| |||| || | ||| | | | | |||| ||| ||| ||| ||||||||||| ||||| ||||||||||| || | | ||||||||||||||| || | | || | | | |
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggta----aattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-

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|32842295|gb|CD981976.1|CD981976
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGCCTTCCAATACGTCCA                         GGTGAAGAACTGTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32839671|gb|CD979352.1|CD979352
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGCCTTCCAATACGTCCA                         GGTGAAGAACTGTGCAAATTCTATTCTCGCTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32836606|gb|CD976284.1|CD976284
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGCCTTCCAATACGTCCA                         GGTGAAGAACTGTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32920863|gb|CF025675.1|CF025675
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCA                         GGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32842543|gb|CD982224.1|CD982224
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGCCTTCCAATACGTCCA                         GGTGAAGAACTGTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|24934304|gb|CA452522.1|CA452522
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCA                         GGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32921366|gb|CF026178.1|CF026178
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCA                         GGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32837496|gb|CD977174.1|CD977174
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGCCTTCCAATACGTCCA                         GGTGAAGAACTGTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|76290171|gb|DV029739.1|DV029739
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCA                         GGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32921013|gb|CF025825.1|CF025825
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCA                         GGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32920651|gb|CF025463.1|CF025463
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCA                         GGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
EST: gi|32838677|gb|CD978355.1|CD978355
EST:     AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGCCTTCCAATACGTCCA                         GGTGAAGAACTGTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC
genomic: AGCCCCCTCCGGATTGTGTCTTAAGTCCAATGGGTCTTCCAATACGTCCAgtaagttgtt ... tggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGGCTGCTCCAATGGGAGTTT
                          tcttgat  putative branch site (score: 4)
 ttttt  putative PPT
 ttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaaataaagcctgtctcacgaataggcactagctagtccttctggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGGCTGCTCCAATGGGAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- -aaataaa
- - - - - - - - - - - - - - cactagc
- - - - - - - - - - - - - - - - - - - -ccttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgcca