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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatgctgctgcgttcagttccttcactgggttctatagtaaacaattagtattttgtatatttaaaatatgcacttgacatttgtagttttatgcacatatctagttactgaactatattattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT

Basic information

species Zea mays
transcript GRMZM2G000749_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 8
--------gttcgtatgctgctgcgttcagttccttcactgggttctatagtaaacaattagtattttgtatatttaaaa--tatgcacttgacatttgtagttttatgcacatatctagttactgaactatattattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
         |  ||||| || | |  ||| ||  |||| |   ||||||  |  | || |    |||||   |  |  ||  |||    || |||||| || |||   ||    |||   |||      | ||||||||||||||||| |||||||| |||||||||| |||||||||||||||   |
gtctgtagctctgtatgatgtt-ctctcaattagttcatttcattctatcattcagaaatgcacttttgctaacctcgaagttattttgttcacatttataattt---gcgtgaatcccattaacacg-tgtattattacagGTTGCAAGAACATGACCTGGATGCAAAACAGCTGGCTGTTGTATAT
















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|21987416|gb|BQ778944.1|BQ778944
EST:     CTTCTGACAGATACATCCTATCTCTACATATACGG                         GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
genomic: CTTCTGACAGATACATCCTATCTCCACATATACGGgttcgtatgc ... attattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
EST: gi|211021453|gb|FL457596.1|FL457596
EST:     TTCTATGAGAAGGAGCTTYTGACAGATACATCCTATCTCCACATATACGG                         GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
genomic: TTCTATGAGAAGGAGCTTCTGACAGATACATCCTATCTCCACATATACGGgttcgtatgc ... attattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
EST: gi|60341236|gb|DN208209.1|DN208209
EST:     TTCTATGAGAAGGAGCTTCTGACAGATACATCCTATCTCCACATATACGG                         GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
genomic: TTCTATGAGAAGGAGCTTCTGACAGATACATCCTATCTCCACATATACGGgttcgtatgc ... attattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
EST: gi|88756696|gb|DY540837.1|DY540837
EST:     GGAGCTTCTGACAGATACATCCTATCTCCACATATACGG                         GTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
genomic: GGAGCTTCTGACAGATACATCCTATCTCCACATATACGGgttcgtatgc ... attattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgacatttgtagttttatgcacatatctagttactgaactatattattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT
 acttgac  putative branch site (score: 4)
                                     tgaactatattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtatgctgctgcgttcagttccttcactgggttctatagtaaacaattagtattttgtatatttaaaatatgcacttgacatttgtagttttatgcacatatctagttactgaactatattattacagGTTGCAGGAACATGAACTGGATGCAAGACAGCTGGCTGTTGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT