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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG

Basic information

species Zea mays
transcript GRMZM2G145595_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
||     |  |  || |  ||||   ||| | |||||  |   |||  | |    | |     ||||       |   | || |||||  |    |||||||||||| ||||| |||||||| |||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||
gtggcacattctagttgcatgttgg-gtttcacttttcattagttaagatatctttggat-catcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
|| || |  |  |||    ||      ||| | |||| |   | |   ||| || |       | ||| |             |  ||  |  | ||    ||||||| |||| |||||||| || ||||| ||||| ||| | |||||||||||||| ||||||||||||||||| ||||
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgttg-----ctgatttag------------agtatggaatgata----gGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatg-cagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                          |||  |||    |||   | ||| |||  |       | | | |   ||| |||  | | |  |   || |||  |||| ||| ||||||||||||| || ||||| ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||
--------------------------gtttgtctcaatttctcatgcaataattatccctccctgactta---ttgttactgacataggatgtggaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatg-cagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                          |||  |||    |||      || |||  |       | | | |   ||| |||  | | |  |   || |||  |||| ||| ||||||| ||||| || ||||| ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||
--------------------------gtttgtctcaacttctcaagtaataattatccctccctgactta---ttgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagt---ttgctacataaacattaaccggtatg-cagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                                  |||||| | | |  |||    |     | |   ||       ||| |||  |   |      || |||  |||||||| |||| ||||| || || ||| | ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||
---------------------------------gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
             || | || ||  |     |   || || |||  ||| | |  ||    ||| |         |||||  |  || |    |||    |||||||  | || || || ||||| |||||||||||||| || ||||||||||||||||| || || |||||||| || |
---------gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaa---------gctactgagtcactc-ttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                ||  |||    || |   |   | ||||| |     | ||  ||| ||| ||| | | ||||| ||  |  |  ||  ||    ||||||| || || || || || || ||||||||||||||  | |||||||| ||||||||||| || |||||||| || |
----------------gtcggttttatttgcatatacataccttttcc----ttgtcagcaattctttcta-tatgctaaattcatttctacttgtg-atagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaa--gtttgctacataaacattaaccggtatgc-agGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                            |    | |  |||  ||||||  |   |     | |   | |   | ||| |||  | |    |     | |   |||||||| | || ||||| || || ||||| ||||||||  | ||||||||||||||||| || ||||||||||| ||||
---------------------------gtctgttataattctcttacaagcacactttttgtgtggcttagccgattgttactgacatggaactttttttattagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------gtatgctaaacc-tgtagtgtgttactgttactcttttgttcctttac-----aacaatgg----taggcatttcattcaagtttgctacataaaca----ttaac--cggtatgc-agGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                                     |||  || |    | | || | ||   || ||  | | |||    |       ||| | |     | ||||     || |   |    ||  |||      ||     |||| | | |||| ||  |||| || || ||||| ||||| ||||| ||| | ||||||||||||||||| ||||| ||||| || || |
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtat-ttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG

upper sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------gtatgctaaacctgtagtg--tgttactgttactcttttgttcctttac---------aacaatg---gtaggcatttcattc---aagttt--gctacataaacatt---aaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                         | | || |  || |  ||  || |||| ||  | ||    |   || |         ||| |||    | ||| |||  |     |||||     ||  | | ||||   | | |   ||||||| ||  | || ||||| ||||| ||||| ||||| ||| | ||||||||||||||||| ||||| ||||| || || |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtgcagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG

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|13249876|gb|BG360781.1|BG360781
EST:     TTGTTCCTGTTGATGAGCGGATGCAAGTTATGGATGCAACTGGCAATGTG                         GTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCT
genomic: TTGTTCCTGTTGATGAGCGGATGCAAGTTATGGATGCAACTGGCAATGTGgtatgctaaa ... cggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
                                      cattaac  putative branch site (score: 2)
                              tacataaacattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA