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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTGTATGTGCCAACAAATCATCTATACATCGGTGACATATTTCTGGTGAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagttgatgcctatcctctattattatgccacgtggcaactttccttgaaatcattgttgtttttctcatctagtcaattttgcattacaaaaa...

Basic information

species Zea mays
transcript GRMZM2G149662_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149662_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 5'ss of exon 5
AGTGTGTATGTGCCAACAAATCATCTATACATCGGTGACATATTTCTGGTGAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagttgat---gcctatcctctat-tatta-tgccacgtggcaactttccttgaaatcattgttgtttttctcatctagtcaattttgcattacaaaaa-----------------------------------------------------------------------------------------
|| || |||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| |||  | |     ||   || |||   |||| |  || ||| |  | |||   |    ||  ||  ||  || ||| ||| | |  | |||||  |  | || | |                                                                                         
AGCGTTTATGTGCCAACAAATCATCTTTACATTGGTGACATATTTCTGGTGAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtgctatt-ttactggttt-ctcctgtgcttaatttctctctgcatagagtggatgataaaaccttcctgaagtcaatcgacccatgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcag

upper sequence: GRMZM2G149662_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 6
AGTGTGTATGTGCCAACAAATCATCTATACATCGGTGACATATTTCTGGTGAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagttgatgcct-atcctctattattatgccacgtggcaactttccttgaaatcattgttgtttttctcatctagtcaattttgcat-tacaaaaa
||||| | ||| || || ||||||||||| || ||||| |||||| |||| || ||  | || || |||||||| ||| | |||||||||||||| ||||||| | |   |   |  | || |  |   |   | ||  ||       |  | |   ||  | |||     | |          || ||| || || |  | 
AGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGACCAAATCTTTCCATTCGAGAAGGCATTGgtaggttctctttcggttgattcattgccaa-gtaccttgtttatgtatctcctattatgctcgttaacaatgtatatggagagatattgtatctatatga-

upper sequence: GRMZM2G149662_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 6
AGTGTGTATGTGCCAACAAATCATCTATACATCGGTGACATATTTCTGGTGAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacg----gtagttgatgcctatcctctattattatgccacgtggcaactttccttgaaatcattgttgtttttctcatctagtcaattttgcattacaaaaa
||||| | ||| || ||||| ||||||||||| ||||| |||||||| || |||||  |||||||||| ||||| ||| | || ||||||||||| || |||||     ||  ||| | |  | ||||||||  | |          |||     |  |      |||  |  ||  | |    ||  ||| ||| ||    | 
AGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGACCAAATCTGTCTATTCGAGAAGGCATAGgtacattctgtttttgctcctcaccctctattcctttcttgttacaaaaccacattgcaggcttgtgtcatcatttccttaacatctttttggcaataattcag

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|91053026|gb|EB163444.1|EB163444
EST:     GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTG                         AAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG
genomic: GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagt ... gtttctgcagAAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG
EST: gi|148956825|gb|EC902729.2|EC902729
EST:     GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTG                         AAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG
genomic: GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagt ... gtttctgcagAAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG
EST: gi|71440103|gb|DR821153.1|DR821153
EST:     AACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGA-TTNG                         AAATAATTGTGTCAGGAGGAATGACCATGCC
genomic: AACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATT-Ggtacggtagt ... gtttctgcagAAATAATTGTGTCAGGAGGAATGACCATGCC
EST: gi|78077279|gb|DV505713.1|DV505713
EST:     GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTG                         AAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCCCTGG
genomic: GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagt ... gtttctgcagAAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG
EST: gi|71772305|gb|DR970241.1|DR970241
EST:     GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTG                         AAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG
genomic: GAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagt ... gtttctgcagAAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGTGTATGTGCCAACAAATCATCTATACATCGGTGACATATTTCTGGTGAACTCTGAGGAGATCATAAGACCTAATTTATCCATTCGAGAAGGAATTGgtacggtagttgatgcctatcctctattattatgccacgtggcaactttccttgaaatcattgttgtttttctcatctagtcaattttgcattacaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA