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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTGCTTTAAAACAACTAAGGAAGTCATTGGTGATTAGAGCGAAACCCATGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccagtttcatgtttctaattctcaacaagtgtagctgtgagcctgtgacttttatcaatttttgcataagtcatggttattgttgagggtatag...

Basic information

species Zea mays
transcript GRMZM2G121176_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121176_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g58480.1 (Oryza sativa), 5'ss of exon 6
CGTTGCTTTAAAACAACTAAGGAAGTCATTGGTGATTAGAGCGAAACCCATGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattcc-agtttc--atgtttc----taattctcaacaagtgtagctgtgagcctgtgacttttatcaatttttgcataagtcatggttattgttgagggtatag
|| |||||||||||||| ||||| || || || || || || ||||||||||||||||| |||||||| || || |||||||||||||| ||||||||| ||| | |||| |||||| | || | | | |||| ||||| ||| | | || |||| | ||| | || | | | | | | |
AACAGCCTTAAAACAACTAAGAAAGTCCTTAGTCATCAGGGCAAAGCCCATGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctgaatttctgatgttttgtgtttcttttggaaacatgtacttgtga--ttgtcagtcttggcaatgtggagatatat--tgctaacttctaggagga---

upper sequence: GRMZM2G121176_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G32860.1 (Glycine max), 5'ss of exon 6
CGTTGCTTTAAAACAACTAAGGAAGTCATTGGTGATTAGAGCGAAACCCATGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccagtt-tcatgtttctaattctcaacaagtgtagctgtgagcctg-tgacttttatcaattttt-gcataagtcatggttattgttgagggtatag
| ||| | || || ||||||||| | ||| ||| | || ||||||||||| || || ||||||||||| || |||| |||| |||||||||| | ||| | | || |||| | | || || ||| | || | | | | | |||| || | || || | | | | |
GGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAAGCAAGCCCTATGCCAAGCTTTTACCATGAAGGGCCCCCTCCTAAGGTTGAATTGAAGAAGgtttgtagtgttcttgtacttttaatagt-atcatgtatagggttcagtttaatcattaaaaacaatgttgagtttatgttaagctctcaaaccaaatttc--

upper sequence: GRMZM2G121176_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G32860.4 (Glycine max), 5'ss of exon 6
-----------CGTTGCTTTAAAACAACTAAGGAAGTCATTGGTGATTAGAGCGAAACCCATGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccagtt-tcatgtttctaattctcaacaagtgtagctgtgagcctg-tgacttttatcaattttt-gcataagtcatggttattgttgagggtatag
| ||| | || || ||||||||| | ||| ||| | || ||||||||||| || || ||||||||||| || |||| |||| |||||||||| | ||| | | || |||| | | || || ||| | || | | | | | |||| || | || || | | |
GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAAGCAAGCCCTATGCCAAGCTTTTACCATGAAGGGCCCCCTCCTAAGgttgaattgaagaaggtttgtagtgttcttgtacttttaatagt-atcatgtatagggttcagtttaatcattaaaaacaatgttgagtttatgttaagct-----------------

upper sequence: GRMZM2G121176_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0020g04880.t01 (Vitis vinifera), 5'ss of exon 7
CGTTGCTTTAAAACAACTAAGGAAGTCATTGGTGATTAGAGCGAAACCCATGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccagtttcatgtttctaattctcaacaagtgtagctgtgagcctgtgactttta----tcaatttttgcataagtcatggttattgttgagggtatag
| || | || ||| | || ||| ||| || ||| || | || ||||||||||||||||| ||||| || ||||| ||||||||||| || |||||| | | | || | | | | | | | || | | || | | || || ||| | ||||| | |
GGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAGGCAAGCCCAATGCCAAGCTTCTATCATGAAGGACCACCACCCAAGGCTGAACTAAAAAAGgtaccacatgctcttggtctatggaatt-atgggtttcttttatacatacaggaagtgcacagttccactagtgtgaaaagaatgtaaaaggttgaagaca---

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|211203600|gb|FL469064.1|FL469064
EST:     TGCCGAGCTTCTATCAAGAAGGGCCCCCWCCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|60358448|gb|DN225421.1|DN225421
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|76912444|gb|DV164735.1|DV164735
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|17930498|gb|BM267458.1|BM267458
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|60352413|gb|DN219386.1|DN219386
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|71441125|gb|DR822175.1|DR822175
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|14243387|gb|BG841044.2|BG841044
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|211056169|gb|FL127767.1|FL127767
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAT                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|78120261|gb|DV538645.1|DV538645
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|60343498|gb|DN210471.1|DN210471
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
EST: gi|116829398|gb|EC867304.1|EC867304
EST:     TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAG                         GTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG
genomic: TGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccag ... ttatgtcaagGTGCCTCCTACCCGTGCCAAATCGCCAAAGTTTACAAGTTCAAGGAGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTGCTTTAAAACAACTAAGGAAGTCATTGGTGATTAGAGCGAAACCCATGCCAAGCTTCTATCAAGAAGGGCCCCCACCAAAGGCTGAACTGAAGAAGgtaattccagtttcatgtttctaattctcaacaagtgtagctgtgagcctgtgacttttatcaatttttgcataagtcatggttattgttgagggtatag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG