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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcatggggttgacttcgttatcattctaataatatcataagtatttttctaccaatgcgacttttgttaataatgatgttccatggttcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTTCATGTGGGGAGCTCAA

Basic information

species Zea mays
transcript GRMZM2G088140_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g13170.2 (Oryza sativa), 3'ss of exon 3
-------ggttcatggggttgacttcg-ttatcattctaataatatcataagtatttttctaccaatgcgacttttgtta-ataatgatgttccatggttcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTTCATGTGGGGAGCTCAA
            |||   ||  ||  | ||    |||| |||  ||   |   ||||    |  ||       | |||||  || | |   ||| |   | ||| ||||| |||||| ||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||| ||||||||||||||| 
aatggataaaaaatgacattatctcagattgcagttctcatagcatgcgacagattt----agaaagatag--tatgttatgtactcactctcctt---tttttagcagGGATATCCTCCAATTCCACCACATGGCTTCTTTCCATCACCTGTGGCGTCAAGCCCACAGGGTCATCCTTACATGTGGGGAGCTCAG

upper sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 3'ss of exon 3
ggttcatggggttgacttcgttatcattcta-ataatatcataagtatttttctaccaa--tgcgacttttgttaataatg-atgttccatggttctttt-gcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTTCATGTGGGGAGCTCAA
   | |  || |  |    |  || ||   | ||   |       ||   | | ||  |  |   |   | ||   | ||| |    |  |  || |||| ||||| |||||| ||||| ||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||| ||||||||||||||| 
--cttaatggataaaaaatgacattatctcagattgcagttctcatagcatgcgacagatttagaaagatagtatgttatgtactcactctcctttttttagCAGGGATATCCTCCAATTCCACCACATGGCTTCTTTCCATCACCTGTGGCGTCAAGCCCACAGGGTCATCCTTACATGTGGGGAGCTCAG
















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|71442579|gb|DR823629.1|DR823629
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCGCCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211355419|gb|FL036287.1|FL036287
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211353027|gb|FL036283.1|FL036283
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211353024|gb|FL036280.1|FL036280
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211353025|gb|FL036281.1|FL036281
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|9952446|gb|BE639029.1|BE639029
EST:     TATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTTCCCTCACCTGGGGCATCA
genomic: TATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|91056940|gb|EB167358.1|EB167358
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|91873165|gb|EB403122.1|EB403122
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211353026|gb|FL036282.1|FL036282
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211355416|gb|FL036284.1|FL036284
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211355418|gb|FL036286.1|FL036286
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|60355311|gb|DN222284.1|DN222284
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211353023|gb|FL036279.1|FL036279
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211355417|gb|FL036285.1|FL036285
EST:     TCAGGTGCTGCAATACCACCTGTYYNCTCCNCGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: TCAGGTGCTGCAATACCACCTGTTTA-TCCA-GATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|71772545|gb|DR970476.1|DR970476
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
EST: gi|211353577|gb|FL066645.1|FL066645
EST:     CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAG                         GCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA
genomic: CCTCAGGTGCTGCAATACCACCTGTTTATCCAGATTGGTCTAGCTTCCAGgtgagcgtga ... tcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctaccaatgcgacttttgttaataatgatgttccatggttcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTTCATGTGGGGAGCTCAA
                      tgttaat  putative branch site (score: 3)
                                            ttcttttgc  putative PPT
                   ttttgttaataatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttcatggggttgacttcgttatcattctaataatatcataagtatttttctaccaatgcgacttttgttaataatgatgttccatggttcttttgcagGCATATCCCCCAATCCCACCACATGGATTCTTCCCCTCACCTGTGGCATCAAGTCCACAGGGTCATCCTTTCATGTGGGGAGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA