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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgcaagctactccccctccctccatttcaagttacagtgttagtatcagagatggtaatacccgttcttgtttcttcctgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTGCACCATCCGAAATGCGACGTCTGCCTTCAGTTT

Basic information

species Zea mays
transcript GRMZM2G151934_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151934_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g16090.2 (Oryza sativa), 3'ss of exon 4
gcatgcaagctac--tccccctccctccatttcaagttaca-gtgttagtatcagagatggtaatacccgttcttgtttcttcctgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTGCACCATCCGAAATGCGACGTCTGCCTTCAGTTT
| |  |   || |  | |   |       | | ||| |    |||||    |       || | |  | |||  |  ||  | |||||  ||||||||| |||||  ||||||||||||||||||||||||||||||||||||| || || || || || |||||||||||||| |||
gtaacctttctgcaattcagtttagaatgtctgaaggtgtgtgtgttcaggtgttctcaggaagtgacagtt--tactttattctgtttcccagTTCACCTTGCTAGGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTTCATCACCCAAAGTGTGACGTCTGCCTTCAATTT
















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|211091867|gb|FL133027.1|FL133027
EST:     CTCAGTGCTTCCGCTGCAACTCCTGCGGCCACCCTATCCGTGAGACCGAG                         TTCACATTACTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTG
genomic: CTCAGTGCTTCCGCTGCAACTCCTGCGGCCACCCTATCCGTGAGACCGAGgcatgcaagc ... tgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTG
EST: gi|13558939|gb|BG550294.1|BG550294
EST:     CTCAGTGCTTCCGCTGCAACTCCTGCGGCCACCCTATCCGTGAGACCGAG                         TTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTG
genomic: CTCAGTGCTTCCGCTGCAACTCCTGCGGCCACCCTATCCGTGAGACCGAGgcatgcaagc ... tgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtgttagtatcagagatggtaatacccgttcttgtttcttcctgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTGCACCATCCGAAATGCGACGTCTGCCTTCAGTTT
                         tacccgttcttgtttc  CT-rich tract
      ttagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgcaagctactccccctccctccatttcaagttacagtgttagtatcagagatggtaatacccgttcttgtttcttcctgttctccagTTCACATTGCTGAGTACAGATCCATACCACAAGCTGTGCTACAAGGAGCTGCACCATCCGAAATGCGACGTCTGCCTTCAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC