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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagatcttgcacttgcactaggcacaattcccatgtgtgaatgaatatgatgttgttttacatgggaagaataaaaaaatatatttgttttatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTTCCAAAATCTGTTATGCATTTCCAGACTTGGAGAATAG

Basic information

species Zea mays
transcript GRMZM2G477146_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G477146_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 2
gagatcttgcacttgcactaggcacaattcccatgtgtgaatgaatatgatgttgttttacatgggaagaata---aaaaaatatatttgttttatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTTCCAAAATCTGTTATGCATTTCCAGACTTGGAGAATAG
    | || |   |   || || | |   |   ||||| |     |  |       |  |  |  | | ||||    |  | | | | | | |||||    ||||||| ||||||||  |||  ||||||| | | || ||||| ||||| ||||| || || ||||||||||| || |||||||||||||
--attttttcgtcttatctgggtatataacatttgtgtaacgttgttgggaacaaatacaattctggaaaatatgtgatgattttgtgtatcttatt-attagAGAGAGAAGCTTTCGACAACCAACAACAATCAAGGCAATGACAAATTTGTTCCGAAGTCAGTTATGCATTTTCAAACTTGGAGAATAG
















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|78106037|gb|DV524455.1|DV524455
EST:     GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAG                         AGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
genomic: GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAGgtggatatta ... tatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
EST: gi|67033412|gb|CO462161.1|CO462161
EST:     GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAG                         AGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
genomic: GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAGgtggatatta ... tatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
EST: gi|76918522|gb|DV167332.1|DV167332
EST:     GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAG                         AGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
genomic: GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAGgtggatatta ... tatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
EST: gi|71332502|gb|DR803214.1|DR803214
EST:     GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAG                         AGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT
genomic: GTGTTGCCATAAACTTTGGTACTAACCTTCTGAAGTTGGGCCATGATCAGgtggatatta ... tatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatgttgttttacatgggaagaataaaaaaatatatttgttttatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTTCCAAAATCTGTTATGCATTTCCAGACTTGGAGAATAG
                                      tttgtttt  CT-rich tract
                atgggaagaataaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagatcttgcacttgcactaggcacaattcccatgtgtgaatgaatatgatgttgttttacatgggaagaataaaaaaatatatttgttttatttggcagAGAGAAAAGCTTTCCTCAATTAACAACAGTGAGGGAAATGAAAAATTCGTTCCAAAATCTGTTATGCATTTCCAGACTTGGAGAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA