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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcttgagatttatgattctttacttcaaaagttgttgaattttgtatttattttagacacagtgtctgttactgttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG

Basic information

species Zea mays
transcript GRMZM2G052277_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g06930.1 (Oryza sativa), 3'ss of exon 7
---gtttcttgagatttatgattcttt------acttcaaaagttgttgaattttgta-tttattttagac--acagtgtctgttactgttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
   ||||||  ||||| |  ||| |||      | || ||     | ||  || |  | || ||| |||||  ||||  |   | ||||||||| || |||||||||||||||||||||| ||||||||||| |||||| |||| || ||||| || ||||| ||||  ||||||||||||||||||||||||||| |||
gttgtttctccagattgaatattattttaaatgatttaaactaccgatgggttatacaattcattctagactaacagcattactcactgttttgctcaagGTAATGACTGCACACCCTGAATGTGCTACATTAGACACATCAATTCTCGATGCTCTGCATATTATGCGCGATGGCAAATTCTTGCATATTCCTGTTGTTG

upper sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------gtttcttgagatttatgattctttacttcaaaagttgttgaattttgtatttattttagacacagtgtctgttact-gttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
                                                                 |||||  |  || || || |||  |  |    ||    | |  | |   | | ||    |   |  |  | |||  ||||     |||| |||||| || ||||  | |||||  |  | || |||||||| ||||||||||| ||||| |||||| |||| || ||||| ||| |||||||  | |
gtggctatgattttattttgtgaagtaaccatacaggaaattggtttattctgtgatgtcttttcttcttccggcttgtgcttattttttctaggtattcagaattaatttgactttcttctttattcttcccttcacttattttttgttagGTGATGACTCCAAACCCACAATGTGCATCTCTAGAGACAACAATTCTTGATGCACTGCATATGATGCATAATGGGAAGTTCTTACATCTTCCTGTGGTGG

upper sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G00560.3 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------gtttcttgagatttatgattctttacttcaaaagttgttgaattttgtatttattttagacacagtgtctgttactgttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
                                                                      ||||||  | ||  |  |  |||  | | |||  | || |    ||  || |||||   |    ||  | || |  || | ||  ||||||||||| || |||| || |||||  || | || ||||| || || |||||||| ||||| ||||||||||| |||||||| ||| |||||||  | |
gttgttatttcattttaatatttattttttggaagtgacttgagtggaaagagggtcgttgtgagaggcctttcttttgtttggttctgattttttgctaaa--tattcagaactgagttgatttt---cttcttgattcttccctttctaatgtagGTAATGACTCCAAACCCAGATTGTGCATCAATAGATACAACGATACTGGATGCACTGCATATGATGCATGATGGGAAATTCTTACATCTTCCTGTGGTAG

upper sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtttcttgagatttatgattctttacttcaaaa-gttgttgaattttgtatttattttagacacagtgtctgttactgttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
                |  ||    ||||   ||| |  || |  | |    |   | ||||| |||   |     || | | ||||  | |  | ||| |||| |||||| || ||||||| || || || ||||| ||||||||||||||||| ||||| || |||||||| || || || || ||| |||||||| | |
cttgaaacgagagacctaatggatcttatagctctctctttgatcatgcaagttcttgttgtacttagcatgatttcact-tgtgttttt-tccttatctagGTGATGACTCCAAACCCTGAATGCGCAACCTTGGAGACAACAATCCTTGATGCGCTACACATAATGCATGACGGGAAGTTTTTACATCTTCCTGTTGTAG

upper sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S86_26V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------gtttcttgagatttatga--ttctttacttcaaaagttgttgaattttgtatttattttagacac-agtgtctgttactgttttga-------------tccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
                                                               ||||| | | |  |  ||||||        | | ||  |||  | |  || ||   ||  |  |   |||| |   ||||||             | ||||| |||||  |  | ||||| ||||||   || || || ||  |  | ||||| || |||||||||||||||||||||||| | ||| |||| |||   |
gtccgatgtgctaacatccactgtgctttctatgggtaccgatttgaatggaaaggcgaaggccttgaaaatgagaaagttctttttaattttactagtgcaatcatatgcttgttcgtgatcctggcagctgtcataattttgaattgaaggacctatgcagGTCATGACACCCAATCCTGAGTGTGCTGGTTTTGATACCACCCTTGTGGATGCGCTTCATATCATGCATGATGGCAAATTCCTCCATCTTCCAGTTACAG

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: 23 (upstream exon), 47 (downstream exon)
Score: 13

CCCAAGGGATGTGCTGATGCGTGTTGTGGCCCAAAATCTTTCTCCTGAGTTAACTCTAGTAGAAAAGgtttcttgag ... tttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG


Block sizes: 23 (upstream exon), 42 (downstream exon)
Score: 6

CCCAAGGGATGTGCTGATGCGTGTTGTGGCCCAAAATCTTTCTCCTGAGTTAACTCTAGTAGAAAAGgtttcttgag ... tttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG


Block sizes: 22 (upstream exon), 43 (downstream exon)
Score: 9

CCCAAGGGATGTGCTGATGCGTGTTGTGGCCCAAAATCTTTCTCCTGAGTTAACTCTAGTAGAAAAGgtttcttgag ... tttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG


Block sizes: 19 (upstream exon), 42 (downstream exon)
Score: 17

CCCAAGGGATGTGCTGATGCGTGTTGTGGCCCAAAATCTTTCTCCTGAGTTAACTCTAGTAGAAAAGgtttcttgag ... tttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttgaattttgtatttattttagacacagtgtctgttactgttttgatccagGTAATGACTGCACACCCTGACTGTGCTACATTGGACACAACAATCCTTGATGCACTACATATCATGCATGATGGCAAATTCTTGCATATTCCTGTTCTTG
                                            ttttgat  putative branch site (score: 17)
                                         ctgtttt  CT-rich tract
     tgaattttgtatttat  TA-rich tract