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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggctaaccctaatgggccggcagcccaacagtggtgccggcctacacacactcacacacatagtctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG

Basic information

species Zea mays
transcript GRMZM2G167886_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167886_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
cggctaaccctaatgggccggcagcccaacagtggtg-ccggcctacacacactcacac-acata-gtcta---acaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG
      ||  |   |   ||         ||||  || |       | || |||  ||  | ||| | |||    | | ||  |||  | | || |||| |||||||||||| ||||||||||||||||||||||||||||| | |||||||  | ||| ||||||||||| |||||||||||||||||||||||  |||||||||
------actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG

upper sequence: GRMZM2G167886_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
cggctaaccctaatgggccggcagcccaacagtggtgccggcctacacacactcaca-cacatag-tctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG
                    | |   |   | || | |  |   |  ||   ||| | |    || | |||||   | | |  |||| |    | | |  || | ||  |||||||||| ||||||||||| ||||| || || |||  ||  || ||||| || ||||| |||||||||||||| ||||||  ||||||||
--------------------gtaaagcctta-tgctactagtacatccatgttcagaacttggagatataacacagaacttgtttgtgtgggccggtc--agATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

upper sequence: GRMZM2G167886_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------cggctaaccctaatgg--gccggcagcccaacagtggtgccggcctacacacactcacacacatagtctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG
                                                                          || |  |  |  |     ||||   | ||| |  | |  || |  | |     |    | | | ||||  |      || |  |||||   |     |||| ||  |||||||||| ||||||||||| ||||| ||||| ||||  |  || ||||| ||||| || |||||||||||      |||    |||||||
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttctctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacactcacacacatagtctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG
                  gtctaac  putative branch site (score: 2)
                                       ttttccact  putative PPT
                            tatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggctaaccctaatgggccggcagcccaacagtggtgccggcctacacacactcacacacatagtctaacaagtatcattgttgttttccactgccatagGTGTATCGAGTTTCAGACATGGAGCTTGTAAGAGTTCTTCCTAGTGTAGGAGAGGAAGTCAATGTTGCATGTTTTCATCCTTCCCCTGGATCAGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA