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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttttaatgttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC

Basic information

species Zea mays
transcript GRMZM2G046005_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G06460.1 (Glycine max), 3'ss of exon 6
tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttt--taatgttttctgatttgc-ttggtattgc-tctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
   | ||| ||     |     || |   |||  |||  ||| | | | |   | |  | | |||  || | | | ||  ||||| || || | |   || |||||||||||  | |||||||||||  | |||||  | || ||| ||||||  ||||||||||| |||||||| |||||||| |||||  | ||||| || |
---aactaacatcctcatcttttttttttgttg-ttatgataaaatgtgattatgggctgtatttcttattatctgctattttgcctttgtctggtaccttcagGAGAGTGACGTGAAGTGGGCTTCAAGATGGGATGCTTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCTATTGTTAACTCATTAATGATTGTTC

upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G11780.1 (Glycine max), 3'ss of exon 6
tgaatctatcacatgaactgcgttg-tcaagttacttaaca-tacattttaaaatttgagtttgttttaatgttttctgatttgc--ttggtattgctc---tgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
      |   |   ||    | ||  |||   || |   |  | | || |   |||    | | || | || || | |||  |||  ||    ||||     | ||||||||| || | |||||||||||  | |||||  |||| ||| | ||||  ||||| |||||||||||||| || |||||||||||  | ||||| || |
------tccaaggggagtcaccttcctcatcctattctcctcttccttctcttattctcatct-ttgtcatcttctttgacctgcctttacctttgcctacattcagGAGAGTAATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
---tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttttaatgttttctgatttgctt--ggtattgctc---tgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
   ||  |||  ||    |   | ||  ||   || ||   | | |  ||    |||    | | || | || || | |||  |||||      ||||     | |||||||||||| | |||||||||||  | |||||  |||| ||| | ||||  ||||| |||||||||||||| || |||||||||||  | ||||| || |
tattgtttcttccatccaagtggagtcatc---ttcctcttcctcctctt----attctcatct-ttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttt--taatgttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
   |    | |  | | | || || |   |||  |||  ||| | | | |   | |  | | |||  || | | | ||  |    ||||       || |||||||||||| | |||||||||||  | |||||  |||| ||| ||||||  ||||||||||| |||||||| || ||||| |||||  | ||||| || |
-agagaattaatgttatccgcctttttttgttg-ttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC

upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
-------tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaat-ttgagtttgttttaatgtt-ttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
           | |  |  || |  |   |   ||  |   ||    |   |   | | | ||| |||  | ||     | || ||||||    | |  || ||| ||||| |||||  | |||||||| ||| | |||||  | ||  | || ||||  ||  ||||||||||||||||||||||||| |||||||| |||||||| |
gcaagttcttgtttgactaatcagtt-tatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctgatg-tcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC

upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 6
----------tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttttaatgttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
            | | ||| | |   | ||  ||  | | | || |    |  | |  |     |||  ||  | || || | ||  || ||||||||||      ||||||||||||| | || ||||| ||||| ||||| |||||| |  | |||   ||||||||||||||||||||||| ||||| || ||| | ||||| || |
gtaagaccacatactttataataaataatgattttgccattaacctg-tgtgtactacaggcaatgatattcctgtattgctgtc--atgtgcttggtat------gcagGAGAGTGATGTGAAATGGGCCTCTCGATGGGATACCTACCTTCTGATGGCCGATGATCAAATTCACTGGTTTTCAATTGTCAATTCTTTGATGATTGTTC

upper sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------tgaatctatcacatgaactgcgt----tgtcaagttacttaacatacattttaaaat---ttgagtttgttttaat--gttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
                                                                                     | | ||  |   |     |  ||    ||||| | ||||   ||    | | || ||   |  || || |   |          ||  |||||| |   |||| ||||||| ||||| ||||||||||| ||||||||||| || || ||||| |||| ||||||||||||||| ||||| || ||||| ||||| |||||||| || |
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtca-gctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttg---tgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaaatttgagtttgttttaatgttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
                           ttctgat  putative branch site (score: 3)
                                            ttgctct  putative PPT
             tttgttttaatgtttt  TA-rich tract