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

...actttgtttcatatggcaaacaataaatgtgttatttagctagcttctacatgtgtttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATG

Basic information

species Zea mays
transcript GRMZM2G095323_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 6
-actttgtttcatatggc-aaacaataaatgtgttatttagctagcttctacatgtgt-ttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATG
 || ||| ||| |||||  |||||||| ||||| |||  |   ||| | | |  |  |  ||   || |  |   |||       | | |    |    | ||||||||||||| ||||||||||||||||||||||| |   ||||||||||||||||||
taccttggttcttatggttaaacaatagatgtgatatacattgagcattttctggcctactgatggaaattatctaactcagttttgcttctgct---aatagAGCCTTGCAGATAGTTGCTTTCCTATTAATCAAGGGCAATCTGCCAGCCGTCTTCATG
















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|148956175|gb|EC901959.2|EC901959
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACCAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCC
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCC
EST: gi|71770155|gb|DR968092.1|DR968092
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAA
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAA
EST: gi|76293362|gb|DV032930.1|DV032930
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71439253|gb|DR820303.1|DR820303
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71310796|gb|DR791700.1|DR791700
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71773093|gb|DR971011.1|DR971011
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|74233328|gb|DT641242.1|DT641242
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|78116974|gb|DV535361.1|DV535361
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|78115630|gb|DV534018.1|DV534018
EST:     AA-GTAAATGCAATGCAGCTGCAGCTACCAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
EST: gi|71428073|gb|DR809123.1|DR809123
EST:     NNNGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAG                         AGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT
genomic: AAAGTAAATGCAATGCAGCTGCAGCTACAAGGAATCGTCATCTTTGTGAGgttcttatca ... tttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacatgtgtttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATG
                              atgtaac  putative branch site (score: 3)
                                         tacattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttgtttcatatggcaaacaataaatgtgttatttagctagcttctacatgtgtttgtgagatagcaagcaacatgtaactccctacatttacgacagAGCCTTGCAGACAGTTGCTTTCCTATTAATCAAGGTCTTGCTGCCAGCCGTCTTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC