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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgtacatcttgagctttgttccgtcgataccgtaattccttgttctaaatcttgtgctgtgtgatcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAGGCAAGTTCAAGCGAGTTTGAGATAAGCAGTGACCGAAGAGAGTCGGGGC

Basic information

species Zea mays
transcript GRMZM2G010953_T01
intron # 5
splice site 3'
intron type U2

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|149070090|gb|EE158490.2|EE158490
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|89755645|gb|DY685992.1|DY685992
EST:     TGGGTCAGGTTGTTTGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|83279064|gb|DV943072.1|DV943072
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|60354736|gb|DN221709.1|DN221709
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|113607860|gb|DW778049.1|DW778049
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|88749325|gb|DY533466.1|DY533466
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|148994591|gb|EE034155.2|EE034155
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|18384770|gb|BM417969.1|BM417969
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAG
EST: gi|149079749|gb|EE168749.2|EE168749
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|88752191|gb|DY536332.1|DY536332
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGC-ACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|148995005|gb|EE034340.2|EE034340
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|78121330|gb|DV539714.1|DV539714
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|91871890|gb|EB401847.1|EB401847
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|89759882|gb|DY688555.1|DY688555
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|149107202|gb|EE189088.2|EE189088
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTCCCTTCACGGGAG                         GACCGCCGGACCCGGAGAGGCCACAGCACCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|76932839|gb|DV173197.1|DV173197
EST:     GGGTCAGGTTGTTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: GGGTCAGGTTG-TTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|30087517|gb|CB885723.1|CB885723
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|31358946|gb|CD443303.1|CD443303
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGTCGGAGCCGGAGAGGCCACAGCAGCAACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
EST: gi|149110970|gb|EE294469.2|EE294469
EST:     TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAG                         GACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG
genomic: TGGGTCAGGTTGTTCGGATGCTCGAGGCAGAAGACGTGCCTTCACGGGAGgtttgttgta ... tcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtcgataccgtaattccttgttctaaatcttgtgctgtgtgatcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAGGCAAGTTCAAGCGAGTTTGAGATAAGCAGTGACCGAAGAGAGTCGGGGC
                       ttctaaa  putative branch site (score: 2)
                                             tcctct  putative PPT
                       ttctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgtacatcttgagctttgttccgtcgataccgtaattccttgttctaaatcttgtgctgtgtgatcctctgaagGACCGCCGGAGCCGGAGAGGCCACAGCAGCCACGCAGACAACGAGTCCAAGGCAAGTTCAAGCGAGTTTGAGATAAGCAGTGACCGAAGAGAGTCGGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA