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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatag

Basic information

species Zea mays
transcript GRMZM2G178822_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 5
GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatag
||| || ||||| ||||| |||||||||||||||   |||||||||||||||||||              ||     |||||| | ||| || |||       ||   || |  ||    || || | ||  ||   | |      | |||| ||   ||
GTACCGAGCACCTGAAGTATTGCTCCAGTCATCTATCTATGATTCTGCAGTTGgta--------------aagtttctactatctactttgtattttgg----cacatatagtacatactaagtcatgattggatgatcccct-ttttgccaacttgcag
















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|60345317|gb|DN212290.1|DN212290
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|31361016|gb|CD445373.1|CD445373
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|67015254|gb|CO444003.1|CO444003
EST:     TCGGGCACCAGNAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|60352824|gb|DN219797.1|DN219797
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|211493408|gb|FL041695.1|FL041695
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatag

- - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - CTGCAG