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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcttaacacagtgatgaataatctgatcatgacttatgcttagagtttgttcttgaatttttgtctatccattctgattctggactgtttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGACAGGCTGGAACAAGGGCAAATCAGCAACTTTCCTGCTGGGTTGTAGGGCC

Basic information

species Zea mays
transcript GRMZM2G030144_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030144_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 18
aaagcttaacacagtgatgaataatctgatcatgacttatgcttagagtttgttcttgaatttttgtctatccattctgattctggactgtttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGACAGGCTGGAACAAGGGCAAATCAGCAACTTTCCTGCTGGGTTGTAGGGCC
 |     |||    || || | || | |  ||| ||| | | | |   ||  |||| || || |  |   |    || | ||||| | | |    | |||||||| ||||| ||||||||||||||  ||||||||||||| ||||||||||||||||| ||||||||||||| ||| ||||||||||| ||||||    
catagacaactatttggtgcacaaacagtccatcactaaggttcaatattctttctagacttgtgattcctaatctccgtttctgaattttaccgcacagAAACCCCTTGCGATGCGTATCCGGATAACTTACAAAGTGAACGGTGAGGACAGGCTGGAGCAAGGGCAAATCAACAATTTTCCTGCTGGATTGTAGTTTG
















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|31363240|gb|CD447597.1|CD447597
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGGGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|91876800|gb|EB406757.1|EB406757
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|31362862|gb|CD447219.1|CD447219
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|113701558|gb|EE679062.1|EE679062
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|60345980|gb|DN212953.1|DN212953
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|71433259|gb|DR814309.1|DR814309
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGGGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|91876799|gb|EB406756.1|EB406756
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|213178150|gb|FM186361.1|FM186361
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC
EST: gi|88751809|gb|DY535950.1|DY535950
EST:     ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAG                         AAACCACTTGCAATGCGTATCCAGATGTCTTACAAAGTGAATGGAGAGGAC
genomic: ATGGGTCAGTTACACAAAGCCTCAGTGTCACCAACAACCAGCATGGCCAGgttattaaag ... tttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttgttcttgaatttttgtctatccattctgattctggactgtttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGACAGGCTGGAACAAGGGCAAATCAGCAACTTTCCTGCTGGGTTGTAGGGCC
                             ttctgat  putative branch site (score: 3)
                                             tttgcctc  putative PPT
          ttgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagcttaacacagtgatgaataatctgatcatgacttatgcttagagtttgttcttgaatttttgtctatccattctgattctggactgtttgcctcagAAACCACTTGCAATGCGTATCCGGATGTCTTACAAAGTGAATGGTGAGGACAGGCTGGAACAAGGGCAAATCAGCAACTTTCCTGCTGGGTTGTAGGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - -aacacag
- - - - - - - tgatgaa
- - - - - - - - - - - - - - - catgact
- - - - - - - - - - - - - - - - - - - atgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggactg