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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttggtctatgtatctgttcttccactgaattgtagtggttttgaattatcctcgatatctttatcaaatgcctctctaacactggctctgatcttttgtgctatcgaagggctgtggtgaccgccaaccaatccagttctgaactaacattgttgctctatctgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTTGATCAATCTGTGAAGCTATAAGCATGTGCTGCTAGAGTAACCAAGGCAA

Basic information

species Zea mays
transcript GRMZM2G031572_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031572_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 13
gtcagtttggtctatgtatctgttcttccactgaattgtagtggttttgaattatcctc-gatatctttatcaaatgcctctctaacactggctctgatcttttgtgctatcgaagggctgtg-----gtgaccgccaa---------------ccaatccagttctgaac--taacattgttgctctatctgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTTGATCAATCTGTGAAGCTAT-AAGCATGTGCTGCTAGAGTAACCAAGGCAA
||  |||| | || |  | || || | | | |||| | ||||| ||   ||  |      || |  | || | ||| | ||  ||  | | | ||||| ||| ||   |     |   || ||     |||||   ||                | ||| || || ||  |  | ||||  |||||||| ||   | |||||||| ||||| ||||||| |||||| || ||||||||||||||| ||   |||| |     |  |||||  || ||| || |   |  |  |  |   || 
gttggttttggctgtccagctattatactattgaactatagtgattgcaaaaaaaaaaaagaaagttataactaatacatccatattagttgttctgagcttctgcttttctcgatcactctgacttcgtgacaaacacatttgcagttcacttcaaattcaattttggtcaatgacatctttgctctaccta-atctcagGACACGACAATGAGCCATTGCTGGGCAGTAGATGGAGCATAGCTACTTACTGATTACCTGCTCGAGCTACCAACCATATGTTCAAAAGGCCATGAGTACA-
















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|76291128|gb|DV030696.1|DV030696
EST:     GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAG                         GACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
genomic: GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAGgtcagtttgg ... tgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
EST: gi|211191456|gb|FL473730.1|FL473730
EST:     GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAG                         GACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
genomic: GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAGgtcagtttgg ... tgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
EST: gi|71441297|gb|DR822347.1|DR822347
EST:     GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAG                         GACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
genomic: GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAGgtcagtttgg ... tgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
EST: gi|67038480|gb|CO464800.1|CO464800
EST:     GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCNAGAGCANG                         GACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
genomic: GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAGgtcagtttgg ... tgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT
EST: gi|166651878|gb|EG116747.1|EG116747
EST:     ACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAG                         GACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGC
genomic: ACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAGgtcagtttgg ... tgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGC
EST: gi|31355151|gb|CD439508.1|CD439508
EST:     GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAG                         GACATGACAAGGAGCCATGGCTGGGAAACAGATGGAGCATAGCTGCTATTT
genomic: GGAGATTGTCGATCACATTGACCTGTGGCTATCAGAATGCCAAGAGCAAGgtcagtttgg ... tgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaccgccaaccaatccagttctgaactaacattgttgctctatctgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTTGATCAATCTGTGAAGCTATAAGCATGTGCTGCTAGAGTAACCAAGGCAA
                        aactaac  putative branch site (score: 1)
                                      ctctatct  putative PPT
                           taacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtttggtctatgtatctgttcttccactgaattgtagtggttttgaattatcctcgatatctttatcaaatgcctctctaacactggctctgatcttttgtgctatcgaagggctgtggtgaccgccaaccaatccagttctgaactaacattgttgctctatctgcgtttcagGACATGACAAGGAGCCATGGCTGGGAAGCAGATGGAGCATAGCTGCTATTTGATCAATCTGTGAAGCTATAAGCATGTGCTGCTAGAGTAACCAAGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT