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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaactggccaacatgaaatttatgctttgtgctttgcatgaacttcgagttgaagcaacaaaaaaaacctgctaacagtttatcttggtcaataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGATCTCGTCACGTGACCACGATTTTCTCTCCGATGTATAGTTAACAAGGAG

Basic information

species Zea mays
transcript GRMZM2G015324_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015324_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g41510.1 (Oryza sativa), 3'ss of exon 7
-gaactggccaacatgaaatttatgct-ttgtgctttgcatgaac-ttcgagttgaagcaacaaaaaaaacctgctaacagtttatcttggtcaataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGATCTCGTCACGTGACCACGATTTTCTCTCCGATGTATAGTTAACAAGGAG
   | ||    ||     |   |   | |||  |||| ||||||| || ||  ||  |||   || |  |  |   |||| | |  ||||    ||  ||||||||||| ||||| ||||| ||||| ||||| || || ||||| || |||||||||||||| ||| |  | || | |  ||| |||| |||||||||  | 
tagattgctagactacttacaaacattcttgcactttccatgaacatttgacatgctgcagataacatcatttctaaacattgttgcttgc---atttttcagGGACATAACAACCACATTTCCCAGTTTTGTATTCAATTCTGAGGTTGATGATCTCGTCACATGATCGTGTTTCTGTTACCGGTGTACAGTTAACAAAAAC
















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|21481223|gb|BQ577906.1|BQ577906
EST:     TNCAC-AGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: T-CACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|76286894|gb|DV026462.1|DV026462
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGATTTTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|9953024|gb|BE639607.1|BE639607
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|71324358|gb|DR798880.1|DR798880
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|211310556|gb|FL467517.1|FL467517
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|18174492|gb|BM349880.1|BM349880
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|113703680|gb|EE681184.1|EE681184
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|12968888|gb|BG265729.1|BG265729
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|78116066|gb|DV534454.1|DV534454
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|6102042|gb|AW126512.1|AW126512
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|67024253|gb|CO453002.1|CO453002
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|87155086|gb|DY399875.1|DY399875
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|74243702|gb|DT651616.1|DT651616
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|21390513|gb|BQ528562.1|BQ528562
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|17931916|gb|BM268876.1|BM268876
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|14311570|gb|BG901325.1|BG901325
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|6227264|gb|AW155863.1|AW155863
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|28985958|gb|CB350899.1|CB350899
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
EST: gi|211383652|gb|FL455014.1|FL455014
EST:     GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAA                         GGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA
genomic: GTCACAAGAAATCCTTCCTTGATGAAGATAATGACTCTGCCATACCTCAAgtaagaatgt ... aataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagttgaagcaacaaaaaaaacctgctaacagtttatcttggtcaataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGATCTCGTCACGTGACCACGATTTTCTCTCCGATGTATAGTTAACAAGGAG
                        tgctaac  putative branch site (score: 1)
           aacaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaactggccaacatgaaatttatgctttgtgctttgcatgaacttcgagttgaagcaacaaaaaaaacctgctaacagtttatcttggtcaataattcagGGACATCACAACAACATTCCCCAGCTTTGTGTTTAACTCTGAAGTCGATGATCTCGTCACGTGACCACGATTTTCTCTCCGATGTATAGTTAACAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - -catgaaa
- - - - - - - - - - tatgctt
- - - - - - - - - - - - - -tgtgctt
- - - - - - - - - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgcta