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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattcgttgtctttataaataagaccatattgtaaatcccaaatcatactccaagttgtcatgtgtttacaattgagtggtaaccccatacacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCAATGTCCAACCCTACTACTAAAG

Basic information

species Zea mays
transcript GRMZM2G085747_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 12
ccattcgttgtctttataaataagaccatattgtaaatcccaaatcatactccaagttgtcatgtgtttacaattgagtggtaaccccat------acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCAATGTCCAACCCTACTACTAAAG
    || |  || |  |  ||   | |   | |   || |  |   ||  ||    || | |  | |  ||| | ||||  ||||   ||      ||  || ||||||||||| |||||||||||||||||||||||||| |||||| ||||||||||||||||||| ||||||||||
---atcatgatcctagtggatttcatctgttagggtatactca--tatgttctctcttataa-atttcaacattggagtcttaactttatctttgtacctctgcagGTTCTCAAGGCTATGAAAGAATCCGATTCCCCTCGTCCTGCAATTTTTGCAATGTCCAACCCAACTACTAAAG
















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|32850587|gb|CD990268.1|CD990268
EST:     CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
genomic: CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagcatac ... acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
EST: gi|74232917|gb|DT640831.1|DT640831
EST:     CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
genomic: CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagcatac ... acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
EST: gi|211281987|gb|FL018040.1|FL018040
EST:     CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAAGCTATGAAAGAATCTGATTCCCCTCGGCCTGCAGTTTTTGCA
genomic: CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagcatac ... acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
EST: gi|26456270|gb|CA827853.1|CA827853
EST:     CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
genomic: CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagcatac ... acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
EST: gi|22819546|gb|BU499636.1|BU499636
EST:     CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAG                         GTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA
genomic: CCCATGTGCTTTTAGGACTATCTGGAGTTGGGGGCATATTTAATGAGGAGgtaagcatac ... acacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactccaagttgtcatgtgtttacaattgagtggtaaccccatacacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCAATGTCCAACCCTACTACTAAAG
                                 tggtaac  putative branch site (score: 2)
                                              cacctcc  putative PPT
                     tttacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattcgttgtctttataaataagaccatattgtaaatcccaaatcatactccaagttgtcatgtgtttacaattgagtggtaaccccatacacctccagGTTCTCAAAGCTATGAAAGAATCCGATTCCCCTCGGCCTGCAGTTTTTGCAATGTCCAACCCTACTACTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG