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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactaatggaacctgagaactattgttgcaccctgtacgaaagattatcatgtgcaactttactcactggtttttgctctcgtactcttgtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATGATATTGGCAAGATTACACATGTATGACTGGATAATACTTCTCCTCCTTG

Basic information

species Zea mays
transcript GRMZM2G024615_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024615_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
atactaatggaacctgagaactattgt-tgcaccctgtacgaaagattatcatgtgcaactttactcactggtttt-tgctctcgt-actcttgtt-tttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATGATATTGGCAAGATTACACATGTATGACTGGATAATACTTCTCCTCCTTG
 |  || |   |    ||    ||||| | |||  |  | | |   || | || |  |||| || | |||   |||    ||| || |   ||||| |||| |||| |||||||||||    ||||| | |||||| || |  ||||||||||  | | |||| ||| | |||||||| ||||||||||||||||| |||||||
-ttttatttttattatagttgcattgtatccacattacatggag--ttgttat-tataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
















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|211212898|gb|FL310336.1|FL310336
EST:     TAGCGGCG-C-ATGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
genomic: TAGCGGCGCCGA-GGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
EST: gi|78119084|gb|DV537468.1|DV537468
EST:     GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
genomic: GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
EST: gi|149100619|gb|EE186707.2|EE186707
EST:     GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
genomic: GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
EST: gi|149099698|gb|EE185747.2|EE185747
EST:     GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
genomic: GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATG
EST: gi|211095464|gb|FK961066.1|FK961066
EST:     GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGG
genomic: GTAGCGGCGCCGAGGGCGATATCGAGGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcatgtgcaactttactcactggtttttgctctcgtactcttgtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATGATATTGGCAAGATTACACATGTATGACTGGATAATACTTCTCCTCCTTG
                tactcac  putative branch site (score: 1)
                                        ctcttgttttt  putative PPT
                                           ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atactaatggaacctgagaactattgttgcaccctgtacgaaagattatcatgtgcaactttactcactggtttttgctctcgtactcttgtttttgcagGAGACAATGGCAGACCAGTTAGGGTCTTACACAATTAGATCCCATGGAATGATATTGGCAAGATTACACATGTATGACTGGATAATACTTCTCCTCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC