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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggaattagcggctaagcatgcgtcgttatcgccatcatttgttgcgtccgtgtcgcgttttgctgtcgtccagcagcgcagcgaagcaacatctcaccaactgattctccatggggggactccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGCGGCCTTGGCTCGCGACCCTTTCGCGGCCATCGACCGGGAGATGGCTGCC

Basic information

species Zea mays
transcript GRMZM2G311665_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 6
gtggaattagcggctaagcatgcgtcgttatcgccatcatttg-----ttgc-gtccgtgtcgcgttttgctgtcgtccagcagcgcagcgaagcaacatctcaccaa-ctgattct-----------ccatgggg---ggactccatg-cagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGCGGCCTTGGCTCGCGACCCTTTCGCGGCCATCGACCGGGAGATGGCTGCC
||||||||    | | | |||      | |||| ||||||||      |||   |    | | |  || ||| ||||||||||  ||||  ||| ||||| ||||||| |||||  |           |||| | |   |  |||  || ||| |  ||||| || ||||||||||||||||| ||||||||||| | ||||||||  || |||||||| ||||||||  |||  ||   ||||||  | |||
gtggaattttgcgattaacatattgtctcatcgtcatcatttaatcatttgttattttcgccacacttagctttcgtccagcaatgcagacaagtaacatttcaccaaactgatcttttttcctctgcccattgtgcttgctctctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC
















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|149096961|gb|EE182760.2|EE182760
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
EST: gi|148937220|gb|EC881402.2|EC881402
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
EST: gi|149088773|gb|EE177898.2|EE177898
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
EST: gi|71771644|gb|DR969581.1|DR969581
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
EST: gi|148962434|gb|EE013289.2|EE013289
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
EST: gi|149072206|gb|EE160452.2|EE160452
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
EST: gi|149015392|gb|EE045235.2|EE045235
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTC
EST: gi|149082408|gb|EE171596.2|EE171596
EST:     GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAG                         CGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC
genomic: GAGGAGTCGTCCGCCGGCGACGCGAGCCCGAACGCGGACAGCGACCAAAGgtggaattag ... ctccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgcagcgaagcaacatctcaccaactgattctccatggggggactccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGCGGCCTTGGCTCGCGACCCTTTCGCGGCCATCGACCGGGAGATGGCTGCC
                        aactgat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggaattagcggctaagcatgcgtcgttatcgccatcatttgttgcgtccgtgtcgcgttttgctgtcgtccagcagcgcagcgaagcaacatctcaccaactgattctccatggggggactccatgcagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGCGGCCTTGGCTCGCGACCCTTTCGCGGCCATCGACCGGGAGATGGCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGTCGCCG