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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaggccctgttttgcttggcacagcaagcatgttcttcttcttcccatgctggtggtaaactatcatcggatcacgcgaaaatttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGC

Basic information

species Zea mays
transcript GRMZM2G123029_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123029_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g04630.3 (Oryza sativa), 3'ss of exon 8
gtgagaggccctgttttgct--tggcacagcaagcatgttcttcttcttcccatgctggtggtaaactatcatcggatcacgcgaaaatttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGC
  |  ||  | |  | |  |  |    ||  |  ||||    |  ||||   |   || || ||   | |  ||   |   || |||||||| |||||| | |||||||||||||| ||||  ||||||||| |||| || ||||  ||||| || |  ||| |||||||||| |||||||||||||||||||| |||
--gttagttcattatctagtaattttccaatatacatggaactactcttttgaatatg-tgata---tgtattcttgtttggcaaaaatttc-tgcagCAATGGGATTGAATCTGTTGTCGACAAAGAAAACTTGGGTTCTGATGCTATGTGTTCAGTTTGTGAGATGGCTGTTGTGTGGATAGAGAACCAGCTACGC
















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|149100422|gb|EE186497.2|EE186497
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|211114340|gb|FL479352.1|FL479352
EST:     CGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTTGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: CGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|7204603|gb|AW559186.1|AW559186
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|149078277|gb|EE167036.2|EE167036
EST:     GGGTGCAGCCAGGTTGGTCTGTGGGTGTTTGATGGCGCTTGATTTGTCAG                         GGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|6827002|gb|AW330645.1|AW330645
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTTGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|78109241|gb|DV527657.1|DV527657
EST:     GGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTTGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|40303709|gb|CK348096.1|CK348096
EST:     GTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTTGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|148980773|gb|EE027343.2|EE027343
EST:     -GGGCAGGCCAGGTTGGTTTGTGGGTGTTCGATGGCGCTCGATCTGTCAG                         GGAGGGGATTGAATTTTTCGTCGGGAAAGAAAACCTGGGGTCAGATGTCAT
genomic: TGTGCA-GCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|110520668|gb|EE024852.1|EE024852
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|32844397|gb|CD984078.1|CD984078
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|211401889|gb|FL450336.1|FL450336
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         GGA-GGGATTTGAATCTGT-GTCGGGAAAGAAAACCT-GGCTTCAGATGTC
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGA-TTGAATCTGTCGTCGGGAAAGAAAACCTGGGC-TCAGATGTC
EST: gi|60358971|gb|DN225944.1|DN225944
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|91876727|gb|EB406684.1|EB406684
EST:     TGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: TGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|91876845|gb|EB406802.1|EB406802
EST:     CAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: CAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|32923207|gb|CF028019.1|CF028019
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTTGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|32844224|gb|CD983905.1|CD983905
EST:     GCGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|32845458|gb|CD985139.1|CD985139
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|32844408|gb|CD984089.1|CD984089
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
EST: gi|148987680|gb|EE031561.2|EE031561
EST:     GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG                         CGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT
genomic: GTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAGgtgagaggcc ... tttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttcccatgctggtggtaaactatcatcggatcacgcgaaaatttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGC
                                             tttcctgc  CT-rich tract
                                         aaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaggccctgttttgcttggcacagcaagcatgttcttcttcttcccatgctggtggtaaactatcatcggatcacgcgaaaatttcctgcagCGAGGGGATTGAATCTGTCGTCGGGAAAGAAAACCTGGGCTCAGATGTCATGTGCTCGGCCTGTCAGATGGCTGTCGTGTGGATAGAGAACCAGCTCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC