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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagttgctttcatcacctaaacagagtttctcttatttatgtaagggcttccaacatgctttaatacgtctcctgctggtctaattatgaacttaatttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACACCTCGAAAGGGGTCACCTTTGTTAAAGGAACTGTGCTTACATCCTTTGA

Basic information

species Zea mays
transcript GRMZM2G320307_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320307_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g47790.1 (Oryza sativa), 3'ss of exon 5
gtaagtagttgctttcatcacctaaacagagtttctcttatttatgtaagggcttccaacatgctttaatacgtctcctgctggtctaattatgaacttaatttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACACCTCGAAAGGGGTCACCTTTGTTAAAGGAACTGTGCTTACATCCTTTGA
|||||||  || ||  ||    || |||       | |||||| |||  ||   ||  | |||    ||||    |  ||   || |   | ||  || |||      |||||||||||||| |||||||| |||||||| || |||||||| | ||| ||| | || | ||| || || || || |||| | ||| | |||| ||| |  |
gtaagtatctgattgaattcggtataca-------ttttatttttgtggggatctc-gatatg----aatataaatgatgtgtgttt---tgtgttctgaat------gcagTGGGTCGTCTTTTTACACCGAAAATTGCTGAGTTTTATGAGAGCTATTACGCTTCAAGAGGAGTTACTTTCGTCAAAGAAGCTGCGGTTACTTCCATGCA
















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|78112090|gb|DV530486.1|DV530486
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|211343496|gb|FL158171.1|FL158171
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACC
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACC
EST: gi|74239090|gb|DT647004.1|DT647004
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAAATGCAGAATTTTATGAAAACTAC
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTAC
EST: gi|76294433|gb|DV034001.1|DV034001
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|149014462|gb|EE044078.2|EE044078
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|93014386|gb|EB639906.1|EB639906
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAA-TTGCAGAATTTTATGAAAACTACT
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACT
EST: gi|74236111|gb|DT644025.1|DT644025
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACT
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACT
EST: gi|13198566|gb|BG354385.1|BG354385
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|148957305|gb|EC903342.2|EC903342
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|87155794|gb|DY400583.1|DY400583
EST:     GGTTACTAACAAGATAAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAA-TTGCAGAATTTTATGAAA-CTACTA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTA
EST: gi|148969919|gb|EE020823.2|EE020823
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|76015963|gb|DT943133.1|DT943133
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|74233733|gb|DT641647.1|DT641647
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
EST: gi|148949714|gb|EC895192.2|EC895192
EST:     GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCA                         TGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA
genomic: GGTTACTAACAAGATTAGGGTCACCATGGTCTTCCCTGAGAAACACTGCAgtaagtagtt ... ttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgctttaatacgtctcctgctggtctaattatgaacttaatttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACACCTCGAAAGGGGTCACCTTTGTTAAAGGAACTGTGCTTACATCCTTTGA
                                            tttgtct  CT-rich tract
                             taattatgaacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagttgctttcatcacctaaacagagtttctcttatttatgtaagggcttccaacatgctttaatacgtctcctgctggtctaattatgaacttaatttgtctgcagTGGGTCGTCTATTTACACCAAAAATTGCAGAATTTTATGAAAACTACTACACCTCGAAAGGGGTCACCTTTGTTAAAGGAACTGTGCTTACATCCTTTGA

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