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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG

Basic information

species Zea mays
transcript GRMZM2G166091_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgc-----------tcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
||| ||  |   | |  || | |  |  |||  | || ||||||             ||||||   || ||||   |   | |  |  || | |||||  ||| ||| |    ||  |||   |||||||| || ||||| ||||| ||||||||||| ||||| ||||||||||||||||||||||||
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
                                  | || |  |     | | | ||   | | |      | |   || || ||  || |  | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG

upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
            |  ||   |  | ||  | || | |  |  |  ||  |   | ||| | | |  ||         |  ||   || |||   | ||| || |||  || |||| ||||| ||||| ||||||||||| |||||||||||||| |||||||||||||||
-----------gtaaggttttttcttgtgtttcatcacattctgactgcaaagttatggttttttagactcaagaggtttgatt-ttagtc--ctgtctttgttct-tagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG

upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
  |||      | |  ||| |    |     |   ||       | ||||   |  |   |||| |  | || |   |||  || |        ||   |||   | |||||||| ||||||||||||||||| || || ||||| ||||| ||||| ||||| ||||||
acatgttgg--tgctagaaatgg-gtatagcttagaaacgtgccgatcaaacattgtttactatttcttgtgcttgttaattaaatg-------ttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG

upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
    | ||   || |  |  |   | | |||  |||     ||  |  | |  |      |     |  |||   |||        |     | || || | |  | |||||||| ||||| ||||||||||||||| | || |||||||| ||||| ||||||||||||
----ggaattgtttcatacttgcaacgattg--ttagtgatatgccatagttcttgaatacggctcgg-atgaattctggct---ctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG

upper sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgatt-----ttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
                ||| |   ||   | | |||    | | | |  ||||  |   ||      ||    ||  ||||   |||| || |       |||| |    | |||||||| || || ||||||||||||||| | || |||||||| ||||| ||||| ||||||
--------------aagaattttgataaat-ttttagtgacgtagttgtatgtgaacaatcctggaaattgcttcaataaggtggttgttctaacacaacttctctatgtttcagTCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
       atctgat  putative branch site (score: 4)
                                      ttttctgt  putative PPT
                      taagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG