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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

Basic information

species Zea mays
transcript GRMZM5G824405_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 19
gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                             ||  |   |  |  |||   |   ||  | |    ||  || ||||  |     || |       ||||| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | 
----------------------------gtactttttatgatttttcaagctgagctttttccttaaata-atgttgattccatgca------ccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G37520.3 (Glycine max), 3'ss of exon 13
gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaacctttt--cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                            |  | | | | |  | |   | |  |   |    | | | | ||  |||   | ||||   | | |  ||||| |||||  | || |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | 
---------------------------gtacttttaaattttaatggctattcaaggtgagcttttgctttaaataa---tgttgatttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 21
gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaacctttt--cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG-----
                            |  | | | | |  | |   | |  |   |    | | | | ||  |||   | ||||   | | |  ||||| |||||  | || |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || |      
---------------------------gtacttttaaattttaatggctattcaaggtgagcttttgctttaaataa---tgttgatttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAGTAAG

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 13
gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaacctttt--cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
            ||| |  | | | || |  | ||| | |  | |   | |  |   |    | | | | ||  |||   | ||||   | | |  ||||| |||||  |||| |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | 
-----------gcaagtc-tttcatatgtactttcaaattttaatggctattcaaggtgagcttttgctttaaataa---tgttgatttcatatgccagGTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 15
gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatag-tatagttatatgtaaacattttgaaaccttt---tcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                           | ||||| ||  |  | ||||| | |      ||| ||   || |   |||| | | |  |  || |    ||||| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | 
------------------------gcaagtatat-accgtgtactttttatgattgtgctagctacctttttccttaaataatgttgattctatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 14
gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
          || |   ||||     || | | | |  ||    ||   |   ||  | |    ||  || ||||  |     || |       ||||| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | 
----------gcaagtctataacgtgtacttt-ttatgatt--gttcaagctgagctttttccttaaata-atgttgattccatgca------ccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
------------gtctgtaattgccaaat-tatattaaata----ttatatcacaatacattttttgtcaag--aatatagtatagttatatgtaa-acattttgaa---acctttt--------cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
              ||| | || | |||  | |  ||| ||    ||| | |  | |  | ||||  |  |   |  || || | | ||  |   | | || ||||    ||  |||        ||||| ||||| || || ||||||||||| ||||| ||||||||||| ||||| |||||||| || || ||  || | 
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
---gtctgtaattgccaaattatattaaatattatatcaca-atacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttt-tcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
   || |      ||  | ||||  | | |  ||   | || ||   | |||||| ||  || |        |  |  |||||| ||     ||| |  ||||| ||||| || ||||||||||| |||||||| ||||||||||| |||||| ||||  | |  || ||  || ||
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagattt-------ctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG

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|84980594|gb|DW530943.1|DW530943
EST:     TGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGGAC-TATTATGAAAAG                         GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
genomic: TGAAGCTGGTGTACAAGATTTCAAAGAGCGATTG-ACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
EST: gi|211189269|gb|FL030572.1|FL030572
EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGGCCTATTATGAAAAG                         GTCTATGCAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGT
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATG-AACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGT
EST: gi|19437252|gb|BM953662.1|BM953662
EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAG                         GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTG
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTG
EST: gi|5895775|gb|AW037021.1|AW037021
EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAG                         GTCTATGAACCGGNGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
EST: gi|67010650|gb|CO439399.1|CO439399
EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGGCCTATTATGAAAAG                         GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                                              ccttttc  CT-rich tract
             aatatagtatagttat  TA-rich tract