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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG

Basic information

species Zea mays
transcript GRMZM5G876621_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
          | |  ||| ||||| | || |||| |     ||  |   |||   | || || ||     |     || |||| || |  | || |   ||  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||
---------gtacagttctaatctgagatattttcttaatactttattattt---ttatttaata-----ttgtggttaatttgtgct--gcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
||| |||||||   |     ||    ||| ||    |||||   |||    |  ||| | |  ||  | |   ||  || ||| | |||     | || |   | |||||||||||  ||||||   |  |||| |||||||||||||| ||||||||||| || || || |||||  |||||||| ||||||| |||
gtatgagttctgtac-----attgtttatgttc---ctgactaacaactaatatgtc-tat-ttatctttgaacatattttttgtctttcataatctt-tctgtgcagTATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCG

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgca-aagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
      | || ||||  ||  |   | || | ||| | |  || || |||| |     |||      ||          | |   || |||  |||| ||    | |||||||||||  |||| |   |||| || ||||| ||||||||  | |||||||| || ||||||||||||||||||||  |||| || || 
-----tggtcctcgccccc--ttagaaatgtattgacggtgctacagaagtatcttctatggcactaatgggaaggtgctgtacttgatttattttgctgc--ttgcagTATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttattta--tgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
    ||| |  || |   |||   || ||| |  || |   ||     | | | ||| ||| ||   |||   ||  | |  ||  || |   | |  ||     | |||||||||||| | ||  |||| || || ||||| ||||||||||||||  | |||||||||||||||||||| |||||| | ||| | || 
---cgagctggtcacactcaacagaagatcctaggtttttgcta-ggtgatggagtcctgt-ctgagtctctgcagatgagctaactgctacagataatt-----tgcagTATGATGAAGCAGAGCGGAGGAGGGAGATGGCTAAGAACTCCCTTGAACGTTACACACATTATTATGAACGCTGGGCAACGAATGAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
 |||  | |   | |||  | || |    |    |  | | ||     || ||  |    | |||| |    || |   | | | ||||   |   ||| |  | |||||||||||| | ||  ||||||| |||||||| |||||||| |||||  | || |||||||| |||||||| |||||  | ||  | || 
-tagaggctgg-cacttgaattcaagcgacg--agatttatcttttgggtctgttt----tcctagttacaatccagagagtgacgtttacttagtttgagtttgcagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S178_72V6.2 (Physcomitrella patens), 3'ss of exon 10
-----gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
       | ||| |  | ||||        ||       ||   |  | || || |||   | | ||  |       | | || ||    ||||| |||||||    || ||||| |||||| | ||  |||| || |||||||| |||||||| |||||  | ||||||||||| |||||||| |||||  | ||| |||| 
tcaagcaaagagattgttgcttttggctctatcgtccccgttatatat-cagaggttgacgcttatataaa------taagttgata---gttttagtttgttt---ctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 3'ss of exon 10
--gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
   | |   | ||| ||  |   ||   || |  |  |||      || | ||      | || || ||  ||    |  ||  |  | |   |||  || |   | |||||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| |||||||| || |||||  | ||  | || 
agctggtcatactttgcaacaggtcc--tagccatattctaggtgacagaattctttcaaagtccttgaattt---gagctaact--gctacagttcattct---tccagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCT

upper sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 9
gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
                                                       | || |    | |   ||  |   | | ||  |   ||||||       |||||| |||||| |||| ||||| ||||||||||| ||||||||  | |||||||| |||||||| || || ||||||||  | ||  | || 
-----------------------------------------------gtaccaattgatatttacgtttcccttcacggactcatcct---gtttgt----gtaacagTACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

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: 162

GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCGgtaggagttc ... gtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 159

GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCGgtaggagttc ... gtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 141

GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCGgtaggagttc ... gtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 125

GCTATGTCTTGGTCCATGGTCAGAGCATGGAGAGAGGACTGGTGGATTTTATGCTTGTAACCGCTATGAGTCAGCAAGGCAAGAAGGAGCGgtaggagttc ... gtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG
                ttctcaatttatttat  TA-rich tract