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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcattcctgatcttttaagatagtttgcatgcttttagtcattatctctcttttatttgtgctttcattttgttgatttacttatatgagtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

Basic information

species Zea mays
transcript GRMZM2G125556_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125556_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 5
ttcattcctgatcttttaagatagtttgcatgcttttagtcat-tatctctcttttatttgtgctt--tcattttgttgatttacttatatgagtgatcg-cagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
        ||   || |  || |  ||   |  |||  ||||| | |   || ||||||||   ||  ||  |||||     | || |||||||  || | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||| |||||||| ||||||||||| |
---ggctttgcctttctgtgagaagttctttaattt-ggtcatgtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT
















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|76285485|gb|DV025053.1|DV025053
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|93282355|gb|EB674619.1|EB674619
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTTTAGTTTTACG                         GTGGCAATGAAGCTTGCTCTTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211377924|gb|FL095474.1|FL095474
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211041272|gb|FL124819.1|FL124819
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCCTA-TAGAGAGAAATTTATGGA
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCC-TAATAGAGAGAAATTTATGGA
EST: gi|211475759|gb|FL124816.1|FL124816
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211464236|gb|FL298400.1|FL298400
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATT
EST: gi|71771167|gb|DR969104.1|DR969104
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211466762|gb|FL298407.1|FL298407
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211464239|gb|FL298403.1|FL298403
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211249240|gb|FL481701.1|FL481701
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|60400894|gb|DN233701.1|DN233701
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|76283007|gb|DV022575.1|DV022575
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211466767|gb|FL298412.1|FL298412
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGCCAATGAAGCTTGCTCCTA-TAGAGAAAAATT-ATGGAGGGCATTA
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTA
EST: gi|211041276|gb|FL124823.1|FL124823
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211484414|gb|FL480094.1|FL480094
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211475757|gb|FL124814.1|FL124814
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|71421128|gb|DR805308.1|DR805308
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211041270|gb|FL124817.1|FL124817
EST:     CCAAGACTTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|93282356|gb|EB674620.1|EB674620
EST:     CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CCAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
EST: gi|211466760|gb|FL298405.1|FL298405
EST:     CAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACG                         GTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT
genomic: CAAGACTTTGAAGAAATTTCATGGATGGCTTGCCAGTTCTAGTTTTACGgtaggatatt ... gtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcttttatttgtgctttcattttgttgatttacttatatgagtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
                          tgttgat  putative branch site (score: 4)
                      attttgttgatttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcattcctgatcttttaagatagtttgcatgcttttagtcattatctctcttttatttgtgctttcattttgttgatttacttatatgagtgatcgcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACCGGTGACATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT