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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA

Basic information

species Zea mays
transcript GRMZM2G399212_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 10
tgtcacatttgtgcaccagaactattatttgaac-ttaatacactgctaaccat-acccaggaaaaatagttgctgcta----acacctctatgttgacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
     |||   |||||| | |||   |||||  | ||| |    | | ||   | |  ||    |||    ||||   |    ||| || |||| ||||||||||||| |||  ||||||||| || || |||||  |||||| |||||||||||||||||||||||||||||| ||||||||||||||||| ||| |||| ||||
-----catggctgcacc-gtacttgcatttgttcgttagtcttgttccaattgttatgcactttaaaatcgtgctaaaataagacatctttatgctgacattttagGTTGAAGGTACAATTGAGTACATCTGTCGTCATGAAGGAGAAGGTGCAATCCTTGTGTTCCTTACTGGTTGGGATGAAATTTCGAAACTTTTGGATAAGA

upper sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
tgtcacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
|      |  |  ||  |      | |||     |    | | || |    ||||      ||    |    |   |       ||   |||  ||| |||| ||    |||||||| ||||| |||||| ||||||| |  || ||||| ||||| || || |||||||||||||||||||| || || || |||||  
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC

upper sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 10
tgtcacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacatttt-agGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
 ||||  || |  ||  |      | |||     |    |   || |    || |      ||    |    |   |       ||   |||  |||| |||| ||    |||||||| ||||| |||||  ||||||| |  || ||||| ||||| || || |||||||||||||||||||| ||||| || |||||  
agtca-gttagctcaatattttcctgattactgttcctcatgatgattcaaatcctttttgaagtgtgcctgtttcattttagttactatgatgttttcagGTAGAGGCAACAATTGAGTATATATGTCGGAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAGCTGCTTGACAAAC

upper sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
tgtcacatttgtgca-ccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattt-tagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
| ||| ||     || ||  || |     | |  ||| ||| |    |   | |    | | ||      |  |    |  || ||   |||  |||  ||||| |||   ||||||||| ||||||||||| ||||||  ||||| ||||| ||||| ||||| |||||||||||||| ||||| || || || |||||  
tctcaaatgatgacatccctaagtgcacgtcg--cttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG

upper sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S36_206V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------------------------------------------tgtcacatttgtg--caccagaactattatttgaacttaatacactgctaaccat--acccaggaaaaatagttgctgctaacac-ctctatgttgac-attttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
                                                                                          ||     ||||||    | |  |       |||   |  |||| |||||||   |             ||| | | |    |||   |||   |||   |||  |||| ||     || |  || |||| ||     | || |  || |||||||||||||||||| | || || |||||||| |||||||||||  ||||     
gtgcgtattcgcttttcagcataaaaaaccatgcacatccttgttctctttaatagcttttgaagttgtgagtgatgtttggaatcttgttgctcactttgtggtttctattagagaagcttgccttgtatac-ctgctaaatgttagtttgatgggcatattcgttaaccacaagttcttccttggtgattgcagGTAGAGGCAGCACTGCAACATATCTGCGTGAAAGAGGAGGACGGTGCAATCCTTGTGTTCTTGACAGGGTGGGATGAGATTTCGAAGCTGGTGGAGCGTC

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: 48 (upstream exon), 47 (downstream exon)
Score: 49

GACATTGACATTACTAAGGAGTATGGAAATTACAGCAGTTCAACAAGGCAGTCCCTTGAAGCTTGGTCTGCTGCTGAACTAGATTTGAGCCTTgtaagtactg ... gacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32

GACATTGACATTACTAAGGAGTATGGAAATTACAGCAGTTCAACAAGGCAGTCCCTTGAAGCTTGGTCTGCTGCTGAACTAGATTTGAGCCTTgtaagtactg ... gacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 47

GACATTGACATTACTAAGGAGTATGGAAATTACAGCAGTTCAACAAGGCAGTCCCTTGAAGCTTGGTCTGCTGCTGAACTAGATTTGAGCCTTgtaagtactg ... gacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 43

GACATTGACATTACTAAGGAGTATGGAAATTACAGCAGTTCAACAAGGCAGTCCCTTGAAGCTTGGTCTGCTGCTGAACTAGATTTGAGCCTTgtaagtactg ... gacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
               aaaaatagtt  TA-rich tract