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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgaacctccagccatcacagcaattatcttatccttatggagttcgtatttgacctataaaactagtggtttgtttttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG

Basic information

species Zea mays
transcript GRMZM2G340527_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 15
------------------------------------------------gtattgaacctccagccatcacagca-----attatcttatccttatggagttcgtatttgacctataaaactagtggtttgtttttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG
                                                 |||| |  ||  |    |||   ||     |  | ||  |   | | || |  || ||||      |   |||   ||     |    | |||||| |  ||   |||||||||||||||| ||||| |||||||| |||||||| |||||||| ||||||||||| || || |||||  | ||| | ||||  |||||       
gtattattaaggctatgtgaaagcatattcctgaactctatgcagcccatatttattctgtatttgtcatgccatgaaaaagaactgctgtctttagattgtgtttttgca----aggtctacaagtaaacatggtttcatcttggttgat-ttagGGCCTGAAAACTGGGATGTATTATCTACGAACACGAGCAGCTGCTGACGCAATCAAGTTCACAGTTGATACTGCCCTTTTGAAGGCCAATGGA------

upper sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 15
gtattgaacctccagccatcacagcaattatcttatccttatgg-agttcgtatt-tgacctataaaactagtggt-ttgttt-ttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG
||||  ||| ||   |  | |       |     ||   | |    |||| ||   ||   ||  || ||  |  | |||||| |||||  || ||  ||     ||||||||||||| |||||||||||||||||  |||| ||||| |||||||| ||||| |||||||| || ||| |  ||||  ||               
gtatc-aacttctttcacttatgcttgatgatgcatagctgtaatggttcataaagtggtttactaatcttcttatgttgtttcttcctgttcatggaca-caaaagGGCCTGAAAACAGGAATGTACTATCTACGGTCACGGGCTGCAGCTGATGCCATCAAATTTACCGTTGACACCTCTATTCTCCAG---------------

upper sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 15
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 14
gtattgaacctccagccatcacagcaattatcttatccttatggagttcgtatttgacctataaaactagtggtttgtttttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG
                                           |       | |   | ||| |   |  |  | ||  | || | | |    | |||  |||||||| || ||||| ||||||||||||||  | | ||||||||| || || |||||||| || ||||||||  |     |||||               
-------------------------------------------gtaaggacactcagcatattagcgttttc-tatgcctgtcttcaacgaaattaatttcagGGCCTAAAGACTGGTATGTACTATCTACGATCGCAAGCTGCTGCGGACGCTATCAAGTTCACTGTCGATACGGCCTCGTTAAAG---------------

upper sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 15
lower sequence: EFJ20157 (Selaginella moellendorffii), 3'ss of exon 14
gtattgaacctccagccatcacagcaattatcttatccttatggagttcgtatttgacctataaaactagtggtttgtttttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGG-AGAATGGGAATGGG
                                           |       | |   | ||| |   |  |  | ||  | || | | |    | |||  |||||||| || ||||| ||||||||||||||  | | ||||||||| || || |||||||| || ||||||||  |     |||||| || ||   | |   
-------------------------------------------gtaaggacagtcagcatattagcgttttc-tatgcctgtcttcaacgaaattaatttcagGGCCTAAAGACTGGTATGTACTATCTACGATCGCAAGCTGCTGCGGACGCTATCAAGTTCACTGTCGATACGGCCTCGTTAAAGGTAGGATTCTATTTTC

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|211165336|gb|FL103224.1|FL103224
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTG
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTG
EST: gi|4621444|gb|AI612277.1|AI612277
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
EST: gi|76015090|gb|DT942260.1|DT942260
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
EST: gi|211165337|gb|FL103225.1|FL103225
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
EST: gi|76018236|gb|DT945406.1|DT945406
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCA
EST: gi|32930349|gb|CF035161.1|CF035161
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGT
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGT
EST: gi|32932558|gb|CF037370.1|CF037370
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGT
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGT
EST: gi|32919054|gb|CF023866.1|CF023866
EST:     AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAG                         GGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGC
genomic: AAGCAAACTTTGGGAAGCTAACATCACTTCACTTCCATGCTTGGTCCAAGgtattgaacc ... tcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtatttgacctataaaactagtggtttgtttttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG
                                 tcctaat  putative branch site (score: 2)
                                       tcttgttc  CT-rich tract
           tataaaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaacctccagccatcacagcaattatcttatccttatggagttcgtatttgacctataaaactagtggtttgtttttcctaatcttgttcaatgccagGGCCTGAAAACTGGAATGTACTATCTACGCACACGAGCTGCTGCTGATGCAATCAAGTTTACCGTCGATACCACACTTCTAAAGGAGAATGGGAATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA