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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagatattttgagattgtccttcattatatagttcagtactcttaatgatgtttactttcag

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 7
GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtac----taagatattttgagat---------tgtccttcattatatagttcagtactcttaatgatgtttactttcag
||||||||||||||||| || |||||||||||||||||  ||||||||||||||||||||||||||     |  |||| ||     |         ||| |  || |||   ||| |||    ||| || ||||| |||||||
GAGGTTCTTTACTGTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatttgatagttcatagtactatcttgtgttccccaatatggcgttgagttaaattattgttgttttctttcag

upper sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA09G02960.1 (Glycine max), 5'ss of exon 7
GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaag----atattttgagattg--tccttc--attatatagttcagtactcttaa--tgatgtttactttcag-------------------------------------------------------------------
||||| || || ||||||||||| ||||| ||||| |||||  | |||||||||||||| |||||   |||    ||| | | ||||    | ||||   || | || |      ||  ||   | || ||||  || |                                                                    
GAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAGgtttgaagcatgatagtataagataaacttcttctggttttgtaatctgaatctagtatccttatatttagctttattctaatatatttgtataactcattataaattatactgtgattaatatggcatttctctccattgtag

upper sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S233_40V6.1 (Physcomitrella patens), 5'ss of exon 8
GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaag---atattttgagat--tgtccttc-attatatagttcagtactcttaatgatgtttactttcag----------------------------
|| ||  | ||||||||||||||  | |||||||| ||||| ||||||||||| |||||||||||    |     || ||| |  |  |  | ||  | |||  |  |   | |   |||| |     ||| ||                              
GAAGTATTGTACTGTGCAAAGAAGTCGGGTGTGACCCACATTTTGAAAGCTGGTGGAGCTCAGgtttgtaatttgtactttaacgtgttaccttttgactatcaaactatctgcatgtaat-actccaactctcgattcagcataagtcgttcttctatctgtt

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|89758985|gb|DY687956.1|DY687956
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|8516559|gb|BE123284.1|BE123284
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAN                         GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|21331772|gb|BQ487153.1|BQ487153
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCATTATTGGCATGGGGAACTGCATCGTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|23357617|gb|BU645266.1|BU645266
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|38688105|gb|CK145136.1|CK145136
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|71432207|gb|DR813257.1|DR813257
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|76012899|gb|DT940069.1|DT940069
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|211215840|gb|FL096753.1|FL096753
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|32840983|gb|CD980664.1|CD980664
EST:     GAAAGCTGGTGTGACACACATATTGAAAGCTGTAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCGTGCCCAAAG
genomic: GAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
EST: gi|38687960|gb|CK144991.1|CK144991
EST:     GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG                         GCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG
genomic: GTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagat ... ttactttcagGCAATCTCAGCAATGGCATGGGGAACTGCATCTTGCCCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAGgtactaagatattttgagattgtccttcattatatagttcagtactcttaatgatgtttactttcag

- - - - - - -  GCAAAG
- - - - - - - -  AAAGAA
- - - - - - - - - AAGAAA
- - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA