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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccctgcacatttatatcttctgtgtgtttctcgcggtggttctgttcaatgagcacctatttaatcaaatttgcattcacaaatataagtgaatggtgactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACTGTAAGCTGCATTT

Basic information

species Zea mays
transcript GRMZM2G074386_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074386_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g32800.2 (Oryza sativa), 3'ss of exon 5
---------gtaagccctgcacatttat-atcttctgtgtgtttctcgcggtggttctgttcaatgagcacctatttaatcaaatttgca--ttca-----caaatataagtgaatggt-gactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACTGTAAGCTGCATTT
           |||   | |   ||| | | ||    ||||  |   |   || |  |||    ||| || ||  || ||   |  ||||  || |     ||   | || | | || |  ||| |  ||     || |  ||  ||| |  |  ||| |||   |||    |||||||| |||||||| ||||||||| |||||||  ||||| |||| ||||||||||||||||| ||||||||||| ||||||||||||             
gtaaggcactgaagttttactagtttgttacctggcatgtgcattatg-attgatcatgtcatgtgatcatctggttgatttgacatgcaagtttatgtgccacccagaaataagtgctcaactgctgatttgaatagctccac-tagtcctaagaatatttctgatgcatgcagGATGCCGTCACACCTTTGTCGGAGACAGAGGCGGTCGATTTAGTGAAGGATGTGTTTGCATCGGCAACTGAGAGGGACATCTACACT-------------
















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|211399901|gb|FL244537.1|FL244537
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATC
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATC
EST: gi|211399900|gb|FL244536.1|FL244536
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGC-AGG                         GATGCTG-CACACCATTG-CGGAGTCAGAG-CCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|86470251|gb|DY236621.1|DY236621
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|19436694|gb|BM953104.1|BM953104
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATGGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|211287478|gb|FL244420.1|FL244420
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCC
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCC
EST: gi|30087522|gb|CB885728.1|CB885728
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|60337848|gb|DN204821.1|DN204821
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|211298181|gb|FL244493.1|FL244493
EST:     TCCTGGACA-TCAACTAAAATCACCNAGTCCTCTATTGCTCCCTGGCAGG                         GATGCTGTCACACCAT-GTCGGAGTCAGAG-CCATCGATCTA
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTA
EST: gi|211287481|gb|FL244423.1|FL244423
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCAC
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCAC
EST: gi|211296044|gb|FL244478.1|FL244478
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGA
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGA
EST: gi|211300319|gb|FL244504.1|FL244504
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCTCACCATTGTCGGAGCCAGAGGC
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGC
EST: gi|211302454|gb|FL244516.1|FL244516
EST:     TCCTGGACAATCAACTANNATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGGCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|211289619|gb|FL244432.1|FL244432
EST:     TCCTGGACNATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTA
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTA
EST: gi|211291756|gb|FL244444.1|FL244444
EST:     CTGGACAATNNCA-CTAAA-TCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTC
genomic: CTGGACAAT--CAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTC
EST: gi|211296051|gb|FL244485.1|FL244485
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATC
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATC
EST: gi|19436261|gb|BM952671.1|BM952671
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATGGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|9461570|gb|BE453798.1|BE453798
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGCTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|14242727|gb|BG840578.2|BG840578
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|211423763|gb|FL057576.1|FL057576
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         NATGCTGTCACACCATTGTCGGAGTCAGAAGCCATCGATCTAAATTAAGGA
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAG-TTAAGGA
EST: gi|13125904|gb|BG316579.1|BG316579
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATT
EST: gi|31364563|gb|CD448918.1|CD448918
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|211402443|gb|FL244546.1|FL244546
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGAT
EST: gi|28873781|gb|CB329723.1|CB329723
EST:     TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCATT
genomic: TCCTGGACAATCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCATT
EST: gi|211293907|gb|FL244467.1|FL244467
EST:     CCTGGACAAATCA-CTAAAATCAC-AAGTCCTCTATTGCTCCCTGCCAGG                         GATGCTGTCACACCAT
genomic: CCTGGACAA-TCAACTAAAATCACCAAGTCCTCTATTGCTCCCTGCCAGGgtaagccctg ... atgtgcacagGATGCTGTCACACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACTGTAAGCTGCATTT
            cgctaac  putative branch site (score: 2)
                                  aaatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccctgcacatttatatcttctgtgtgtttctcgcggtggttctgttcaatgagcacctatttaatcaaatttgcattcacaaatataagtgaatggtgactacaaataacgctaacagcagatagcctaagaaatcttttcaatgtgcacagGATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGATGTGTTTGCATCTGCAACTGAGAGAGACATCTACACTGTAAGCTGCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC