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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatgcatgtggctcacgttgttcccagtatccttttggacttagattgagtttgatatatggttatgtttattgacacactgctttttggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGGTGGGTATCCTCGTTATTATTCTAATGAAGAGGGCTA

Basic information

species Zea mays
transcript GRMZM2G366935_T07
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 2
tgaatgcatgtggctcacgttg--ttcccagtatccttttggacttagattgagtttgata-tatggttatgtttattgacacactgctttt--tggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGGTGGGTATCCTCGTTATTATTCTAATGAAGAGGGCTA
   ||||   |   |   ||||   |  || || || |  ||  ||| |   | || | |  | ||    ||||  |||| |  || || ||  ||| | |||||| |||||||||||||||||||||||||                                                                         
--gatgc---taattttagttgaaattgcaataaccgtagggctttatagctatttaggttctgtgagattgttcgttgatattcttctcttcttggctatgcagACAAAATCTTGAGCAAAATGGGAGAAG-------------------------------------------------------------------------
















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|211042609|gb|FL405101.1|FL405101
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|93015243|gb|EB640763.1|EB640763
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|211045786|gb|FL411675.1|FL411675
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGYTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|211070907|gb|FL383766.1|FL383766
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|148983054|gb|EE028963.2|EE028963
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|71439614|gb|DR820664.1|DR820664
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|149000442|gb|EE037616.2|EE037616
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
EST: gi|211340986|gb|FL379602.1|FL379602
EST:     CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGAT                         ATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG
genomic: CCGCGACGGACACTACGTCTTCGATCTCGGCGAGAACTTGACCCGCCGATgtgagcgccc ... ggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgagtttgatatatggttatgtttattgacacactgctttttggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGGTGGGTATCCTCGTTATTATTCTAATGAAGAGGGCTA
                          tattgac  putative branch site (score: 2)
                                       ctttttg  putative PPT
                   ttatgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatgcatgtggctcacgttgttcccagtatccttttggacttagattgagtttgatatatggttatgtttattgacacactgctttttggttgtgcagATAAAATCTTGAGCAAAATGGGAGAAGGTTCGGGTTTTCTGCAATCTGTCGTCTCCTCTTCTGGTGGGTATCCTCGTTATTATTCTAATGAAGAGGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG