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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA

Basic information

species Zea mays
transcript AC155496.2_FGT009
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 9
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaaca-tttcttttgtatagattcagtatcctttaaacatctg-----tctggttttgt----agGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
                                                         || | |   | |  | || |  || |     |||||| || |||||||| | | |||| | ||  |||  || ||        | ||||  |||    ||||||||||||||||||||||||||||||| || ||||  |||||||||||||| |||||||||||||| |||||||||||||||||||| || |||||||
--------------------------------------------------------tctatgcctctat-ccattggtggcgtacacgatatcatcaatttcttttatttggatttaatactcttgtaaaataaaatgactttggtgctgttctcagGACATTGAATTATCCAAAGAAATAAATGAGTCTTTCAAGCAATCATCTCAAGCAAGGACAAAGCTTCCATCTGGCATTGAAATGAGTGTTCACGTGCTTA

upper sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
                             || ||| |  | ||  |  | ||  || ||  |    || ||  |||      |    || ||||    ||||      || ||     ||  |||  | |||             |||||||||||||||| |||||||||||||||||||||| ||| ||||| || || ||| |||| ||| | || || |||||||||||||| |||||  | |
-----------------------------atcttttgaatgatgatgctctgacaaacttca----tgaattattatagttcttattaacatcacagcttctgacaactacatctcaaatt-tttgtaaatc-------------agGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA

upper sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 10
gtagcgttagctgttattactatgaatacatttttagtcttatcttattt-tgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
                                    |   ||| | | || ||   | |||   |  |  ||   |   |  | ||    | | | |  || |||| ||||  | || |||  |||         |||  ||    |||||||||||||||| ||||||||||| || || |||| ||| ||||| || ||||||||||| || || || || |||||||||||||| |||||  | |
------------------------------------ggactatatgagttatgatgatctgacaaacttcatgaattactatagctttttt-ttatccattgttttttataactacattattttttt--------tctaattc---agGACATTGAATTATCAAAAGAAATAAACGAGTCCTTCAAACAGTCATCCCAGGCTAGGACAAAACTCCCATCCGGGATTGAAATGAGTGTTCATGTTTTGA

upper sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 9
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggtt-ttgt-----agGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
                                                 ||       |||    |  | |    |  | ||  |||| ||| |  | ||||| | ||      |||  ||    ||  || | ||   || ||||     |||||||||||||||| |||||||||||||| ||||||| ||| ||||| || || ||| |||| ||| | || || |||||||||||||| |||||  | |
-------------------------------------------------ttattgttttgtgtgatgatctgacaaacttca--tgaattatta-tagttcttat-taacatcacagcttctgacaactatgtctcaaattgttgtgaatcagGACATTGAATTATCAAAAGAAATAAATGAGTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA

upper sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 9
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
                                        |||    |  ||   | |||   || | |||   |   |  | ||   || | | |  ||  ||| ||||  | |  |||  |||     | |  ||  ||    |||||||||||||||| ||||||||||| || || ||||  || ||||| || ||||||||||| || || || || |||||||||||||| |||||  | |
--------------------------------------actatgccgtaatgatgatctgacaagctttatgaattattatagcttttat-ttatctgttgctttttataactacgttatttttt-----ttttcctaattc---agGACATTGAATTATCAAAAGAAATAAACGAGTCCTTCAAGCAGTCATCCCAGGCTAGGACAAAACTCCCATCAGGGATTGAAATGAGTGTTCATGTCTTGA

upper sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacct--gtacagttgtatcgttaggt-gcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
                                   | | |||| |   ||||  ||  |   ||||    |||  || | | ||||    ||| | ||  | | |||| |       ||  ||| | ||| |||        ||||  |||||||||||||||| ||||| |||||||| || |||| ||||||||| ||||| |||||||| |||||  | || ||||| |||||||| |||||  | |
-----------------------------------aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaaattattttttatg------caacatcttgtaa-cat--------ttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA

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|32810090|gb|CD962324.1|CD962324
EST:     AAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAG                         GACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCTA
genomic: AAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAA
EST: gi|32935166|gb|CF039978.1|CF039978
EST:     AAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAG                         GACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAA
genomic: AAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAA
EST: gi|61119354|gb|DN560315.1|DN560315
EST:     AAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAG                         GACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAA
genomic: AAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 190

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 100

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 103

CTCAAAACTGAGTGTGGAAGTCAGTTTACCAACAAGCTGGAGGGAATGTTCAAGgtagcgttag ... ggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
         ttttgtata  TA-rich tract