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

gtcagtaggtttgccgtatcaattgacggagtggttctccttcgtccttctgttataaaaatcattcgttccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGTTCACAGCCACGATACTAGATGCGGCGAAATGCAGGGAACTGAAGATGGG

Basic information

species Zea mays
transcript GRMZM2G043893_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043893_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 3
-----------------gtcagtaggtttgccgtatcaattgacggagtggttctcctt----cgtccttctgtt---ataaaaatcattcgttccattc--cagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGTTCACAGCCACGATACTAGATGCGGCGAAATGCAGGGAACTGAAGATGGG
                   |    |     | || | ||||  | |  | | |  | ||     |||    | |    |||  ||   || | | | |||  ||| || ||||||||||| |||  |||| || ||||| |  ||||| |||||||| || || |||||| |||| | || |||||||||||| |||||||||||
gtaaatcactgcattcttcctactgaaacactgtctgaattttctgcatagattccattgcaatgtctgcttatctgaatattaactctttgattctttcttcagCTGTTCTCGCGGAGGAGGCATCGAACATTGCTTCTAGTTACAGTGACGTGTTGACGGCGACGATATTAGACGAGGAGAAATGCAGGGAGCTGAAGATGGG
















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|101393107|gb|EB818484.1|EB818484
EST:     CAGGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGTGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|149001041|gb|EE038290.2|EE038290
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|76913696|gb|DV165228.1|DV165228
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACG
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACG
EST: gi|74236862|gb|DT644776.1|DT644776
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|148958193|gb|EC904398.2|EC904398
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|71436982|gb|DR818032.1|DR818032
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|71758309|gb|DR956246.1|DR956246
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|89252259|gb|DY624045.1|DY624045
EST:     CCTGCCAAGGTCTTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|71318207|gb|DR795866.1|DR795866
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
EST: gi|74236861|gb|DT644775.1|DT644775
EST:     CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTG                         GTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT
genomic: CATGCTTGCGAGAGATCTTGTGAACTCTCCTGCCAATGTCCTTACCCCTGgtcagtaggt ... tccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacggagtggttctccttcgtccttctgttataaaaatcattcgttccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGTTCACAGCCACGATACTAGATGCGGCGAAATGCAGGGAACTGAAGATGGG
 aattgac  putative branch site (score: 3)
                                            ttccattcc  putative PPT
                          tgttataaaaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaggtttgccgtatcaattgacggagtggttctccttcgtccttctgttataaaaatcattcgttccattccagGTGCTCTCGCGGAGGCGGCGGCGAAGATCGCTTCGACGTACAGCGACGTGTTCACAGCCACGATACTAGATGCGGCGAAATGCAGGGAACTGAAGATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG