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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgattaagtcaaatttgttgcattgtgtatgtgaataaattgagcttgtcttgtttatcttatgagctcatctactatgtcttgttactctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g35520.4 (Oryza sativa), 3'ss of exon 7
gcttgattaagtcaaatttgttgcat-tgtgtatgtgaataaattgagcttgtcttgtttatcttatgagctcatctactatgtcttgttactctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG
     || |||  | ||    | ||  ||  | |||   ||   | ||  ||  |||   |  |  ||||||  |  ||  | | ||  |    ||| ||||| ||||| ||||||||||||||||||||||| ||||||| ||||||||| | ||||||||||||||| ||||||
----catgaagcaacatcaactccaagtgcatttgtctttatggttagactggattggacaaatcttgagctttttcaccttttttttcttactttttcagaagAATGGCCCTGGTGCACCTGGTGGGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG

upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 3'ss of exon 7
gcttgattaagtcaaatttgttgcat-tgtgtatgtgaataaattgagcttgtcttgtttatcttatgagctcatctactatgtcttgttactctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG
 ||  || |||  | ||    | ||  ||  | |||   ||   | ||  ||  |||   |  |  ||||||  |  ||  | | ||  |    ||| ||||| ||||| ||||||||||||||||||||||| ||||||| ||||||||| | ||||||||||||||| ||||||
-ctccatgaagcaacatcaactccaagtgcatttgtctttatggttagactggattggacaaatcttgagctttttcaccttttttttcttactttttcagAAGAATGGCCCTGGTGCACCTGGTGGGCAATCGTGGACAGCTGAATGGCTTAAGTTTGATAACAGTTATTTCAAG
















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|4887369|gb|AI677468.1|AI677468
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|7162396|gb|AW520018.1|AW520018
EST:     GGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|60342201|gb|DN209174.1|DN209174
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|24934386|gb|CA452604.1|CA452604
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|71327463|gb|DR800349.1|DR800349
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|67022725|gb|CO451474.1|CO451474
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|7216381|gb|AW562503.1|AW562503
EST:     AAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: AAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|101393103|gb|EB818482.1|EB818482
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|60397958|gb|DN230774.1|DN230774
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|7238058|gb|AW573325.1|AW573325
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|74246091|gb|DT654005.1|DT654005
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|60349847|gb|DN216820.1|DN216820
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|211351874|gb|FK984289.1|FK984289
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|76920121|gb|DV168019.1|DV168019
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|76292512|gb|DV032080.1|DV032080
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|60342528|gb|DN209501.1|DN209501
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|71759931|gb|DR957868.1|DR957868
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|14244899|gb|BG842837.2|BG842837
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|88753851|gb|DY537992.1|DY537992
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
EST: gi|7145161|gb|AW506642.1|AW506642
EST:     GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACT                         AAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG
genomic: GGTCCAGGCCTGAACGGAGTGGCTGGGGGAAACCAGAAACAAAATATACTgtatgttctt ... ctctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttgtcttgtttatcttatgagctcatctactatgtcttgttactctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG
                                     tcttgttactcttt  CT-rich tract
           tttatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgattaagtcaaatttgttgcattgtgtatgtgaataaattgagcttgtcttgtttatcttatgagctcatctactatgtcttgttactctttacagAAAAATGGTCCTGGTGCACCTGGTGGGCAATCATGGACAGTTGAATGGCTGAGGTTTGATAACAGTTACTTCAAG

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