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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagctcttgctgcaagtttatttatatcagttttctgtctatctgtttaactattcatttccaattgccttctcttaaatttcagtcgtgcttcttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG

Basic information

species Zea mays
transcript GRMZM2G077299_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 12
gtaaa--gctcttgctgcaagtttatttatatcagt-tttctgtctatctgtt-taactattcatttccaattgccttctcttaaatttcagtcgtgcttcttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG
|||||   ||| | ||      || | |    |||   ||||   | | |||   || | |  |       || || | | |||||||  |    |  | |||||||||||||||||| ||||||||||||||||||    |||||||  |||||||| ||| ||||||||| ||| ||||||
gtaaactactcatcctcttgagttgtgttctccagcacttctcattctttgtcacaaatgtcaaggctt--ttcccatttattaaattgaaacaat--tccttttttctagGTCTATACTGATTCTAAGACTTTGTTTTCAATGAAGAATACATTTGATAGATCATCTCGTAATGGGCCCAAG

upper sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 12
gtaaa--gctcttgctgca-agtttatttatatcagttttctgtctatctgtttaactattcatttccaattgccttctcttaaatttcagtcgtgcttcttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG
|||||   ||| | ||    ||||   ||||       ||||   | | |    || | |  |  |    || || | | |||||||  | |  | | | |||| |||||||||||| ||||||||||||||||||    ||||||||  ||||||| ||| ||||||||| ||| ||||||
gtaaactactcatcctctggagttctgttatgcagtacttctcattctgtcaccaa-tgtcaaggttt--ttcccatttattaaattctaataattcct-ttttctctagGTCTATACTGATTCTAAGACTTTGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG
















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|32847594|gb|CD987275.1|CD987275
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|213170538|gb|FM181869.1|FM181869
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|116814377|gb|EC856917.1|EC856917
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|12045517|gb|BF727656.1|BF727656
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|32846175|gb|CD985856.1|CD985856
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|6095297|gb|AW119964.1|AW119964
EST:     GGTTCATCTACACCACTTGATCATCCCTGCTGATTTATACCGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACA
genomic: GGTTCATCTACACCACTTGATCATCC-TGCTGATTTATAC-GACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACA
EST: gi|211082959|gb|FL420012.1|FL420012
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|32865761|gb|CF005443.1|CF005443
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|78179997|gb|DV550370.1|DV550370
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|32846927|gb|CD986608.1|CD986608
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|17970148|gb|BM276913.1|BM276913
EST:     GCTGATTTATACGACTTCCAT                         GTGCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAG
genomic: GCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGT-CTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAG
EST: gi|32835529|gb|CD975207.1|CD975207
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|22489289|gb|BU049212.1|BU049212
EST:     GCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: GCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
EST: gi|32846588|gb|CD986269.1|CD986269
EST:     ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCAT                         GTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA
genomic: ATGGTTCATCTACACCACTTGATCATCCTGCTGATTTATACGACTTCCATgtaaagctct ... ttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattcatttccaattgccttctcttaaatttcagtcgtgcttcttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG
 gtttaac  putative branch site (score: 3)
                                    tcgtgcttcttttttc  putative PPT
                       tcttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagctcttgctgcaagtttatttatatcagttttctgtctatctgtttaactattcatttccaattgccttctcttaaatttcagtcgtgcttcttttttctagGTCTATAATGATTCTAAGACTTTGTTCAACATGAAGAGCACATTTGACAGAACATCTCGTAGTGGACCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA