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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccgacaatccaagtttatggatacgcatgaaggtattgatcagaatatatttctgatccgtctgtataactgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT

Basic information

species Zea mays
transcript GRMZM2G099328_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 8
gtaagtgccgacaatccaagtttatggatacgcatgaaggtattgatcagaat-atatttctgatccgtctgtataactgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT
|||||||     | |||| | | | | ||  ||||| | || ||  |  || | | ||| |||||| ||||  |  | ||  | | ||   | ||| | | ||||||||||| || ||  |||| || || ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||| |||| |
gtaagtgaatgaattccatgctca-gaatgtgcatggacgtgttagttggagttacattcctgatctgtcttga--attgagactgttgcat-ttcatacacagATTCCAACGAACAGGAATGGGCTGATCGAATACCGAGCACATCCATTCTGGATGCAAAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTAGGTGTT

upper sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtgccgacaatccaagtttatggatacgcatgaaggtattgatcagaatatatttctgatccgtct---gtataac-tgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT
|| |||   || |  | |  | | | |||    ||     | ||   || ||| | || |      ||     |  |||  || |  ||| |      || | | ||||||| ||||||  || ||| || ||||| ||  | |||||||| || |||||||| ||||| |||||||| |||||   |||||| ||||||||||| |
gtgagt---gatagccaacttctgttgatctctata----ttttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT

upper sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgccgacaatccaagtttatgg-atacgcatgaaggtattgatcagaatatatttctgatccgtctgtataactgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT
   | |    | || | |  | |      ||    ||    | |||       |  |    |||| |    | || | || |||| ||    | | ||   ||||||||| |||||  || |||    |  || ||  ||||||||||||||||||||||  |||||||||| || |||||  ||||||| ||||||||||| |
--cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttc--ccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT

upper sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtgccgacaatccaagtttatggatacgcatgaaggtattgatcagaatatatttctgatccgtctgtataactgcaat---tattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT
   | |    | || | |  | |      | | ||    || ||  |  | || | ||||  |   |    | || |  ||||   | |  |  ||| ||   |||||||||||||||  || ||| || ||||| ||  |||||||||| ||||||||||| ||||||||||| || || ||  ||||||| ||||||||||| |
--tattttgaataaactagatgtgca---atgtatatttgt-ttcttttgtatgtttttcacaaatgatactgtagcatcaatgtatttctttcctttttgtacagATTCCAACAAATGCAGCTGGACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTT

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|211513637|gb|FL388499.1|FL388499
EST:     CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTT                         ATTCCA-CAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
genomic: CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTTgtaagtgccg ... tcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
EST: gi|6020787|gb|AW065715.1|AW065715
EST:     CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTT                         ATTCCAACCAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
genomic: CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTTgtaagtgccg ... tcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
EST: gi|32867973|gb|CF007655.1|CF007655
EST:     CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTT                         ATTCCAACCAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
genomic: CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTTgtaagtgccg ... tcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
EST: gi|71773669|gb|DR971566.1|DR971566
EST:     CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTT                         ATTCCAACCAATAGAGATGGCCTCATTGAATACCGAGCACAT
genomic: CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTTgtaagtgccg ... tcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACAT
EST: gi|76287174|gb|DV026742.1|DV026742
EST:     CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTT                         ATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG
genomic: CCTGCTACAAAGAGTTTTTTCATCCGAAATGCGATGTTTGCAACAACTTTgtaagtgccg ... tcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatatatttctgatccgtctgtataactgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT
                      gtataac  putative branch site (score: 3)
                                     ttatgtcttcttcccc  putative PPT
                                aattattatgtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgccgacaatccaagtttatggatacgcatgaaggtattgatcagaatatatttctgatccgtctgtataactgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC