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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctgctgcttcagtcttatgttcccacttgtgcgtgtgtgtgttgtgtttttttttcttttttgtttcttccattcagttaagccatgcttctctctaacaaagactcttcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCACTTGCAGCCAGGCTAGGGGTTGTGACAG

Basic information

species Zea mays
transcript GRMZM2G069198_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 4
-----------------------gtgcctgctgcttcagtcttatgt-tcccacttgtgcgtgtgtgtgttgtgtttttttttcttttttgtttcttccattcagttaagccatgcttctctctaacaaaga------------ctcttcaattgc-agCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCACTTGCAGCCAGGCTAGGGGTTGTGACAG
                        |  || || |||   |  ||  | ||  |  |         |      |||     ||    ||   | | | |||||||| || | ||||||| ||| |||||||||             ||||   |||| |||||||||||||||||||| |||| || |||||||||||||| ||||||||||||||||| |||||||| || ||||| |
gtgcattactacttctcttctttatagctacttcttttatagtacctatcatatcttctttctcataaagcatgtgacccttgaaattgaatgtatgccattcagatatgtcatgcttatctttaacaaagaaccacaaccgttttcttttgttgccagCTTCTTTGGATCATACTTATTGCGTCATGTGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTG
















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|211420188|gb|FL124226.1|FL124226
EST:     TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG                         CTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
genomic: TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAGgtgcctgctg ... tcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
EST: gi|211049303|gb|FL092984.1|FL092984
EST:     TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG                         CTTCTTTGGATCATACTTGTTGCATCCTGNGCTGCTCTTATTATTCAATCA
genomic: TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAGgtgcctgctg ... tcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
EST: gi|93014188|gb|EB639708.1|EB639708
EST:     TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG                         CTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
genomic: TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAGgtgcctgctg ... tcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
EST: gi|211420191|gb|FL124229.1|FL124229
EST:     TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG                         CTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
genomic: TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAGgtgcctgctg ... tcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
EST: gi|71767113|gb|DR965050.1|DR965050
EST:     TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG                         CTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA
genomic: TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAGgtgcctgctg ... tcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttccattcagttaagccatgcttctctctaacaaagactcttcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCACTTGCAGCCAGGCTAGGGGTTGTGACAG
                             ctctaac  putative branch site (score: 2)
                                         ctcttc  putative PPT
                                taacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctgctgcttcagtcttatgttcccacttgtgcgtgtgtgtgttgtgtttttttttcttttttgtttcttccattcagttaagccatgcttctctctaacaaagactcttcaattgcagCTTCTTTGGATCATACTTGTTGCATCCTGTGCTGCTCTTATTATTCAATCACTTGCAGCCAGGCTAGGGGTTGTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT