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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaactattttatggaatatggaccatgaataccaccataaccatccattcaaattttcagttacattctactgtcttgcataatctattattgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTGACAATTCCTGTTTATGAAA

Basic information

species Zea mays
transcript GRMZM2G457881_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G457881_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g49730.2 (Oryza sativa), 3'ss of exon 11
ccaactattttatggaatatggaccatgaataccaccataaccatccattcaaattttcagt-tacattctactgtcttgcataatctattattgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTGACAATTCCTGTTTATGAAA
              | ||||   |       ||    | ||  | |   |    |    ||   ||  |||| | |  |  |  | ||||||||   |||||||||| |||| ||||||||||||  |||||| ||||  || || |||||||||||||| ||||||||||
--------------gtatattttcagcattaacagtaaaaataacctgctagggtacagagcacaccatctagtatgattaaccacctattatttgtgcagATATATATGGAGTTACAAGATTGGCAGACTGCATTGATGTATTGCAGATTGACAATTCCAGTTTATGAAA
















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|89755657|gb|DY686001.1|DY686001
EST:     ACCATGCTTTCTCAATTACTTTGCTGCACACGTGCGAAACACTATTGAAG                         ATATATCTGGAATTACAAGATTGGTGGGCTGCGTTGACATACTGTAGATTG
genomic: ACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAGgtaaatttca ... attgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTG
EST: gi|211477964|gb|FL457116.1|FL457116
EST:     ACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAG                         ATATATCTGGAATTACAAGATTGGTGGACTGCATTGACATACTGTAGATTG
genomic: ACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAGgtaaatttca ... attgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTG
EST: gi|149023563|gb|EE154541.2|EE154541
EST:     ACCATGCTTTTTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAG                         ATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTG
genomic: ACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAGgtaaatttca ... attgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTG
EST: gi|71322958|gb|DR798156.1|DR798156
EST:     ACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAG                         ATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTG
genomic: ACCATGCTTTCTCAACTACTTTGCTGCACACGTGCGAAACACTATTGAAGgtaaatttca ... attgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattcaaattttcagttacattctactgtcttgcataatctattattgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTGACAATTCCTGTTTATGAAA
                                            tattgac  putative branch site (score: 2)
                                   ataatctattattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaactattttatggaatatggaccatgaataccaccataaccatccattcaaattttcagttacattctactgtcttgcataatctattattgacgcagATATATCTGGAATTACAAGATTGGTGGACTGCGTTGACATACTGTAGATTGACAATTCCTGTTTATGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
ccaacta
- - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - taccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgca