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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

Basic information

species Zea mays
transcript GRMZM2G165418_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
|||| | | | ||||| |||| | ||||||| |||| || ||||||   | |      |||| |     ||     | |||||| | ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||||||||| | ||||||||||||||| |||||
gtgagactttgtcaaccgaatgactaaaaag-aagccatatgatgactgata----cataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
gtgaaattctctcaactgaataattaaaaaggaagctatt-----tgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
|| | |||| |     |  |||| |||  || ||   |||     || |  |  ||   |  |||| |   | || |   |     ||||| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| |||||| | |||||| |||||||||||||  |
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
|| | |||| |     || || |  ||  |  |       || |  |  ||  ||  |||| |   |  | |   |     ||||| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| |||||| | |||||| ||||||| |||||  |
gttagattcccatgtttggatgagcaatga--atttctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
------------------------------------gtgaaattctctcaactgaataattaaa--aaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
                                    |  ||||   |  | ||  |||||| |   |||      |||| ||  | ||   |  ||  | ||  |  | | |      |||| | || ||| |||| || ||||| ||||| || |||||||||||||| ||||| ||||| ||||||  ||| |||||||||||||| ||  |
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagca-acctatataattgatctaagtgtatcattttatccataatgatggtgggactt-gtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
                   ||  ||| ||       || | ||||      |  | | |     |||  |  |||  | |     | | ||  |   | ||||| |||||| | |||||||  |||||||| || ||||||||||||||||| |||||||| ||||| || || ||||| |||||||||||| |
ttctgttatcagctgcaattgggattgtcggtgagaaacagttaagctactaattttgttcaatacagtaacaattcagtg--gagctttctgtgtctgcagCTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
------gtgaaattctctcaactgaataa-------ttaaaaaggaagctat----ttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
      || | ||| ||| | |  | | |       |  | |  |||| | |    ||| ||||||   |      ||||||||  ||| ||   || ||||| |||||||| |||||||| ||||| |||||||||||||||||||| ||||||||||| |||||    ||||||||||||||||||||  |
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttat-accttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
----------gtgaaattctctcaactgaata-attaaaaaggaagctatttgatgaacaaaagtaatgtaattttatga--tat---cactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
           || |   ||     || ||||   | |  ||  || ||   ||          || || | || ||  |  |||   |     || ||||| |||||||| || ||||| ||||| || |||||||||||||| || |||||||||||||||||  | ||||| ||||||||||| ||  |
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
-------gtgaaattctctcaactga-ataattaaaaaggaagctat--ttgatgaacaaaagtaatgtaattttatgatat------cactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
         |   |  | | | |||  || |||     || |   |   |            | |||||| |  ||| |  |       |    || ||||| |  ||| | ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||  | ||||| || |||||||| ||  |
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
-----------------gtgaaattctctcaactgaat-aattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
                  ||||       ||   |||| | ||    | |    | |    || |   || | |   || ||  | |  |   |  || |||||||||||||| || ||||| || ||||| ||||| ||||||||||| ||| | ||||| |||||  | ||||| ||||||||||| ||  |
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgt--ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

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|71419453|gb|DR804773.1|DR804773
EST:     ATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACTTAAG                         CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGT
genomic: ATTCAGGCCCTGTTTCAACCTTCCAAGTCCATGAACATTTAAGACCTAAGgtgaaattct ... ctactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG
        atttgat  putative branch site (score: 5)
                                             ctactttc  putative PPT
                aacaaaagtaatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA