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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagactgagattaagaactgcttagtttaactttgtttagctgctgtagtgtactctttgaatgtttatatgtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

Basic information

species Zea mays
transcript GRMZM2G039811_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
gtacgagactgagat-taagaactgcttagtttaactttgtttagctgct-gtagtgtactctttgaatgttta---tat-gtgatgatttc-atggaacctcaatt-----ttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
|||| ||  |   || |      ||  |  | |  |    || |  || | || |  || ||| | |||||| |   ||| |  |||||||| || ||| ||   |      |||||||||||||| ||||||||||| || |||||||||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC

upper sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
--------gtacgagactga--gattaagaactgcttagtttaactttgtttagctgctgtagtgtactctttgaatgtttatatgtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
         |    |||| |    || |  ||    ||||||    ||  | || | || | |||| |   ||      | |  |||  ||||||    |   || |  | | ||||| |||||  | |||||||| ||  | |||||  | || || |||||||  ||  |||| ||||| |||||||||||||| |||||||| |||||||| |
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtgttcctgtt-----ctcac-tgttttgatttttgcg---ctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC

upper sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 6
gtacgagactgagattaagaactgcttagtttaactttgtttagctgctg--tagtgtactctttgaatgtttatat----gtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
         | |||  |   |||   || |  |   |  ||| ||   |     ||||   ||        | ||||    ||  || | |||||    ||   | | ||||||||||||  | || ||||| || || ||||| ||||||||  ||||| | |||||||| ||||| |||||||| ||||| || ||| | ||||| || |
--------gtaagaccacatactttataataaataatgattttgccattaacctgtgtgtactacaggcaatgatattcctgtattgctgtcatgtg--cttggtat-gcagGAGAGTGATGTGAAATGGGCCTCTCGATGGGATACCTACCTTCTGATGGCCGATGATCAAATTCACTGGTTTTCAATTGTCAATTCTTTGATGATTGTTC

upper sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------gtacgagactgagatta---agaactgcttagtttaactttgtttagctgctgtagtgtact-------ctttgaatgtttatatgtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
                                                                            | || || | |  |       |  |  || ||  ||  |    || ||  |  ||||||          | |   |  |   |    |  | ||         |    | ||||||| ||||| |||||||||||||| || ||||| || ||  |||||||||| |||||||| ||||||||||| || ||||| ||||| |||||||| || |
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagcta-ctagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC

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: 39 (upstream exon), 43 (downstream exon)
Score: 47

TTGTGATCCTCATGCAAGCAAATTTGTCATAAACTCTGATTCTCCTCAGGAAGTTGAAGCTGACAAGGAAATCATATTCACATATGATGTTCATTTTGAGgtacgagact ... aattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 82

TTGTGATCCTCATGCAAGCAAATTTGTCATAAACTCTGATTCTCCTCAGGAAGTTGAAGCTGACAAGGAAATCATATTCACATATGATGTTCATTTTGAGgtacgagact ... aattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 81

TTGTGATCCTCATGCAAGCAAATTTGTCATAAACTCTGATTCTCCTCAGGAAGTTGAAGCTGACAAGGAAATCATATTCACATATGATGTTCATTTTGAGgtacgagact ... aattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 197

TTGTGATCCTCATGCAAGCAAATTTGTCATAAACTCTGATTCTCCTCAGGAAGTTGAAGCTGACAAGGAAATCATATTCACATATGATGTTCATTTTGAGgtacgagact ... aattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtactctttgaatgtttatatgtgatgatttcatggaacctcaattttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC
         tttgaatgtttatat  TA-rich tract