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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgcaaacccttgtagtacaatgtcttgtgtcaaactggcgaagtttccaatactaaaatttctctgtgctaatatactagttatctgtagtgtacctaacagcttgtttagcgaactgatgaactgtatcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCAAGGAAACAG

Basic information

species Zea mays
transcript GRMZM2G092776_T07
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092776_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 9
gtaaatgcaaacccttgtagtacaatgtcttgtgtcaaactggcgaagtttccaatactaaaatttctctgtgctaatatactagttatctgtagtgtacctaacagcttgtttagcgaactga--tgaactgtatcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCAAGGAAACAG
                                             ||  ||  |||    | ||  | | || |  ||||   |||||     |   || | |   | |   ||||| ||   |  | ||||||||| ||||||||||||||||||||||||||||||||| ||||||||||| |||||| |||||||||| ||
--------------------------------------------caaacttttaatgtatatatcccacagtacatatattgcagttaaagacatcctagcaatttgttaacttagccaatcaaaatcaactgtatcttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
















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|110536646|gb|EE040761.1|EE040761
EST:     CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAG                         ATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|67020360|gb|CO449109.1|CO449109
EST:     CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAG                         ATCAGATTAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTTAGGGACTGC
genomic: CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGC
EST: gi|89252188|gb|DY623974.1|DY623974
EST:     CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAG                         ATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|110960194|gb|EE180246.1|EE180246
EST:     TTTTATTGATAGTAAATGGTCTGTTGCTATCGACAG                         ATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: TTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|149106666|gb|EE188560.2|EE188560
EST:     CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAG                         ATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|148966542|gb|EE017566.2|EE017566
EST:     TTGCCGCTACAGATTTTTATTGATAGTAAATGGTTTGTTGCTATCGACAG                         ATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTTTTAAGGGACTGCA
genomic: TTGCCGCTACAGA-TTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|74233198|gb|DT641112.1|DT641112
EST:     CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCCATCGACAG                         ATCAGATAAAGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|211299421|gb|FL314585.1|FL314585
EST:     CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCCATCGACAG                         ATCAGATAAAGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: CTTGCCGCTACAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
EST: gi|91877535|gb|EB407492.1|EB407492
EST:     CAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAG                         ATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA
genomic: CAGATTTTATTGATAGTAAATGGTCTGTTGCTATCGACAGgtaaatgcaa ... atcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgtagtgtacctaacagcttgtttagcgaactgatgaactgtatcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCAAGGAAACAG
                                            tatcctctc  CT-rich tract
                     ttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgcaaacccttgtagtacaatgtcttgtgtcaaactggcgaagtttccaatactaaaatttctctgtgctaatatactagttatctgtagtgtacctaacagcttgtttagcgaactgatgaactgtatcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCAAGGAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA