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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

Basic information

species Zea mays
transcript GRMZM2G054136_T06
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 1
---------------------------------gtaagctactcccggcttttcccacgataggaggtgtttgtgg-gaatatagtatctgatctgtgcg-----cac-----tttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
                                   |    |     || ||||           || | ||| |   |    | |  ||||||  ||| |     | |     ||| ||||||||||||||||||||  ||||||||||||| |||||||| || ||||||||||||||||||||
gtaagacgctcctcgtcgccgttgctggatcccccagatgagctagggattttatggtagggttagatttttttttcgtgggtggcttctgattcgtgtggtttccgccttcgttttcagTTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 1
-----gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT-----------------------------------
     ||     |  ||    |  | ||  | | |||  | |||||| |  ||| |  |   |  | | ||   ||||  ||||||||||| || || ||  |||| |||||||| ||||||||||||||||||||||||| ||||||                                   
gtgttgtctctaaaccctaattgcttccctgtttgga--tttttgtgtgtttatcgc-tgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCTGTAATCATTTCACTCTCTCTTCAATTTTCATTTGT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G31840.2 (Glycine max), 3'ss of exon 1
-----gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
     ||     |  ||    |  | ||  | | |||  | |||||| |  ||| |  |   |  | | ||   ||||  ||||||||||| || || ||  |||| |||||||| ||||||||||||||||||||||||| ||||||
gtgttgtctctaaaccctaattgcttccctgtttgga--tttttgtgtgtttatcgc-tgaaacatattcgatttttctacagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 2
---------------gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
                 |  |||||   |  || | |  ||||     |   ||| ||    ||  | || |  |    |    ||| ||||||||||| ||||| ||  ||||||| || || ||||||||||| |||||||| |||| ||||||
gtttgttgtcctctgaaaccctacttttgctttctgcttcgatttcttgccattg-ggactaattatgtccgcacacaacttcttttgcagTTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 1
-----gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttc--cagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
     ||     |  ||    |  | ||  | | |||  | |||||| |  | | |  |   |  ||| ||   || |  ||||||||||| || || ||  |||| |||||||| ||||||||||||||||||||||||| ||||||
gtgttgtctctgaaccctaattgcttccgtgtttgga--tatttgtgtgtttgtcgc-tgaaacatgttcggttttgctgcagTTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S253_7V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------gtaagctactcccggcttttcccacgataggagg--tgtttgtgggaatatagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
                                                      | || | ||   || ||  |  |  |  | ||     ||    |  | |   || |  |       |    | ||| |||||||||| |||||  |||| ||||||||||||||| | || ||||||||||||   |||||
gtacacgcatacgggggctccctctgccctcccctgtttcctttccatcttcacatgccaatcttcgcattcactgctctctgtgggtcagtttcctgtctttttaatttagttcagttcctggctgcagCTCAACATCGCCAACCCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT

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|211496229|gb|FL154440.1|FL154440
EST:     GCTCGAGCTCCTCGCTCCCTGCGAGTGCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCTTCCACCGGGTG
genomic: GCTCGAGCTCCTCGCTCCCTGCGAGCGCGCGCCGCAACGCCACCATGAAGgtaagctact ... cactttccagTTCAACATCGCGAACCCTTCCACCGGGTG
EST: gi|22521636|gb|BU080447.1|BU080447
EST:     GCGAGCGCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
genomic: GCGAGCGCGCGCCGCAACGCCACCATGAAGgtaagctact ... cactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
EST: gi|211496231|gb|FL154442.1|FL154442
EST:     CTCGAGCTCCTCGCTCCCTGCGAGCGCGCGCCGCAACGCCACCATGGAAC                         TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAAT
genomic: CTCGAGCTCCTCGCTCCCTGCGAGCGCGCGCCGCAACGCCACCATG-AAGgtaagctact ... cactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAAT
EST: gi|149075315|gb|EE163821.2|EE163821
EST:     GCTCGAGCTCCTCGCTCCCTGCGAGCGCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCTCCCTGCGAGCGCGCGCCGCAACGCCACCATGAAGgtaagctact ... cactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT
                               atctgat  putative branch site (score: 4)
                                             cactttcc  putative PPT
                       aatatagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctactcccggcttttcccacgataggaggtgtttgtgggaatatagtatctgatctgtgcgcactttccagTTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC