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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC

Basic information

species Zea mays
transcript GRMZM2G124886_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
||||| | | | |   | ||| |   | || |||||     | ||||||| | |   |              |||  ||     ||||  ||| |  |||  |||     ||| |||| |||||||||||||||| ||||| || ||||||||| ||||||||||||| |||||||| || |||||||||||||| |||||||||||||| |||||| 
gtttgcgat-tttgttccttaca---tttgcttggcatagtttttgcatt-tctaacattt-----------cttggtctggatttgaatgtggtgcccttattt-----aatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 6
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
|| |   |  | | |   ||   | || ||    || |   | ||   ||||||   | | ||    || |    ||  | ||     |  | || |  ||| |||| |      ||||| |||| |||||| ||||||||||| ||||| ||| | ||||  |||   ||||| ||||| |||||||||||||| || ||||||||    || || |
gtatacat-gtgttcttcttgctagttgtgtcctgc-attttctttgtttatttccaaac-acctatgataaaaattaaaaagtaatgtattaatgt--tatcttttcttg----cagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATC

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
gtttgtgttatctccgctttaaaaattctggttg-gccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttt--tgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
    || | ||    |  ||       || |||| | |   |  || | || |||  | ||      | |        | | |  || |  || || |  || | ||    |||||  ||||| |||| |||||| ||||||||||| ||||| ||  | |||| ||||   ||||| ||||| |||||||||||||| || ||||||||   ||| ||||
----gtat-atacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatga-----taaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatt-tggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
               |   | |||    ||||     ||| ||   ||| ||| ||||   | | |     ||     ||||   |  | | | | || | || ||    ||   |||||| |||| ||||||||| || ||||||||||| ||| | |||| ||||   ||||| || || ||||| ||||| ||||| |||||||||   || ||  
---------------gtgctgaaa----tggtcta--acattgaaacatcattatggtttagtccgct--tagtccgctcat---tctacgtttacatgc-atgtt----catcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 6
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgata-tcctattttttgtcaatat-cagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
                 | ||| |  ||      ||    |  ||  ||   || ||     || | |  |  |||   |  | ||  |     || |  |  |  ||||  |||| |||||||||| ||||||||| || ||||||||||| ||||| ||||  |||   ||||| || |||||||| ||||| ||||| || ||||||  ||| || |
--------------gtgtgtaagaggtcca---agcactgagcttttatggcttagt--tagcacgaggtacttttaaaagggttttcttagactaattttcatgcttgttcatattcagATATGGAATCTTGGTTCCCCAGACCCAAATTTTACACTGGATGCTCATCAGAAAGGAGTCAACTGTGTAGATTATTTCACAGGGGGTGATAAACCCTATC

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcatta-tttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
|| ||   |   |   || |    |  || |||  |  || | ||  |  | ||| |   |  || |    ||  |  |  |       || |||||||   ||||          |||||||||| |||||| ||||| ||||| ||||| ||||| |||| ||||   ||||| || || |||||||||||||| || || ||||||  |||||| |
gtatgatctggattttctgttggcaa-cttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttc---------cagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtgtta--tctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
 | |   |||  || | | |||      | |  ||    ||| | || | |  |||  |    | |    | ||  |  | ||   |||||  ||   |||| ||            ||||| |||| ||| || || |||||||||||||| ||  | |||| |||    ||||| || |||||||||||||||||||||||||||||    |||||| 
-tatactttaagtcgctgttttggcggcttt--ttcaatacagtttttc-tcctttacttataaaaaaaaaaag--tcctaatg--ttgatc-tggcgtcctgttc-----------cagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT

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|78107583|gb|DV526001.1|DV526001
EST:     CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAG                         ATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
genomic: CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
EST: gi|50325003|gb|CO520129.1|CO520129
EST:     CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAG                         ATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
genomic: CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
                   gcttgat  putative branch site (score: 5)
                                 tcctattttttgtc  putative PPT
                                    tattttttgtcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG