Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtatgtctttctaatagttattatatacatgaaaactacatatttacagggttgacattatgtgtagtggttaataagcttctgcatgttgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTC

Basic information

species Zea mays
transcript GRMZM2G131324_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 4
agtatgtctttctaatagttattatatacatgaaaact-acatatttacag--ggttgacattatgtgtagtggt--taataagcttctgcatgttgcttttt-agGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTC
   ||||| |||   | ||  ||  ||    |||  || | ||||||      | || || | |  |  | |  |   ||| ||   |  ||| ||| || |  ||||||||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||| ||||||||||||||||| ||||| ||||||||||||||
---atgtccttcccct-gtctttgcatgg--gaattctgagatattttagattgtttaacttcacctaaaatcatgacaatgagagaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC

upper sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 4
agtatgtctttctaatagttattatatacatgaaaactacatatttacagggttgacattatgtgtagtggt--taataagcttctgcatgttgcttttt-agGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTC
  | |   |  |   |||||       |  |   ||  | || ||     | || || | |  |  | |  |   ||| ||   |  ||| ||| || |  ||||||||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||||||||||||||||||||| || || ||| ||||||||||
-atgtccttcccctgtagttgcatgggaattctgaa--atattttagattgtttaacttcacctaaaatcatgacaatgagagaccacatcttgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTC
















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|76293904|gb|DV033472.1|DV033472
EST:     ACAGCTAGAGACCTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|67031739|gb|CO460488.1|CO460488
EST:     ACAGCTAGAGAACTACTTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|32931459|gb|CF036271.1|CF036271
EST:     ACAGCTAGAGAACTACTTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|76016034|gb|DT943204.1|DT943204
EST:     CAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: CAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|71758032|gb|DR955969.1|DR955969
EST:     CAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGA-TGCCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAG
genomic: CAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTG-CCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAG
EST: gi|76010883|gb|DT938053.1|DT938053
EST:     ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|26456742|gb|CA828325.1|CA828325
EST:     ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|78113480|gb|DV531871.1|DV531871
EST:     ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|71758174|gb|DR956111.1|DR956111
EST:     AGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: AGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|211012560|gb|FL439511.1|FL439511
EST:     CAGCTAGAGAACTACTTAGATGATGA-TATCTTTGTGTTTGATTGCCCTG                         GCCAGATTG-ACTCTTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAG
genomic: CAGCTAGAGAACTACCTAGATGATGATTATC-TTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTC-TTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAG
EST: gi|32934477|gb|CF039289.1|CF039289
EST:     ACAGCTAGAGAACTACTTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
EST: gi|60343210|gb|DN210183.1|DN210183
EST:     ACAGCTAGGGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG                         GCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC
genomic: ACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTGgtatattctc ... tgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagggttgacattatgtgtagtggttaataagcttctgcatgttgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTC
                        ggttaat  putative branch site (score: 4)
                                            ttgcttttt  putative PPT
                          ttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtatgtctttctaatagttattatatacatgaaaactacatatttacagggttgacattatgtgtagtggttaataagcttctgcatgttgctttttagGCCAGATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT