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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgctgggacaccttcaacagaatttcatagtatttatttacaaaaacaacgatcctattttttgcgatgcaatgataaaaattcacttctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT

Basic information

species Zea mays
transcript GRMZM2G317346_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G317346_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g04670.1 (Oryza sativa), 3'ss of exon 1
catgctgggacaccttcaacagaatttcatagtatttatttacaaaaacaacgatcctattttttgcg----atgcaatgataaaa----attcacttctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT
|||||   |  |   ||    |  |||  ||||    ||       ||  |   |||| |||| ||||    |  |  ||  |  |    |||||||    | | ||||||||| ||||||||  | ||||||||||||| ||||||||||||||||||||| || || ||||||||||| |||||||| ||||||| ||||||||||
catgccaagctattgtctgtgg--tttattagtcacaatc------aattagcctccttttttatgcgcaaaagactgtggcatgatattattcactctgtcttgcagGTCAAACAGAGAGTTTCTATATCATATTCTAGAGGAAGTCATAAAAGCTGGAGCAACAACACTCAATATCCCAGACACTGTTGGATACACTCTTCCTTAT

upper sequence: GRMZM2G317346_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g04440.2 (Oryza sativa), 3'ss of exon 1
catgctgggacaccttcaacagaatttcatagtatttatttacaaa-aacaacgatcctattttttgcg----atgcaatgata----aaaattcacttctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT
     |   | | |      || || |  ||    ||| | ||||  ||  |   |||| |||| ||||    | ||  ||  |    |  |||||||    | |  |||||||| ||||||||  | |||||||| |||| ||||||||||||||||||||| || || ||||||||||| |||||||| ||||||| ||||||||||
-----ttaaaaaacggaggtagtatgtttta----ttagtcacaatcaattagcctccttttttatgcgcaaaaggctgtggcatgatatgattcactctgtcttgtagGTCAAACAGAGAGTTTCTATATCATATACTAGAGGAAGTCATAAAAGCTGGAGCAACAACACTCAATATCCCAGACACTGTTGGATACACTCTTCCTTAT
















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: 44 (upstream exon), 48 (downstream exon)
Score: 68

AGACGCCCGACCAGGTGGTCACCATTGCCAGGGAGATGGTGGCTTACGCCCGCAGCCTCGGATGCACTGACGTCGAGTTCAGCCCCGAGGACGCCGGCAGgtatagtgtt ... ctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

AGACGCCCGACCAGGTGGTCACCATTGCCAGGGAGATGGTGGCTTACGCCCGCAGCCTCGGATGCACTGACGTCGAGTTCAGCCCCGAGGACGCCGGCAGgtatagtgtt ... ctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 164

AGACGCCCGACCAGGTGGTCACCATTGCCAGGGAGATGGTGGCTTACGCCCGCAGCCTCGGATGCACTGACGTCGAGTTCAGCCCCGAGGACGCCGGCAGgtatagtgtt ... ctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

AGACGCCCGACCAGGTGGTCACCATTGCCAGGGAGATGGTGGCTTACGCCCGCAGCCTCGGATGCACTGACGTCGAGTTCAGCCCCGAGGACGCCGGCAGgtatagtgtt ... ctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacaacgatcctattttttgcgatgcaatgataaaaattcacttctccctccagGTCAAATAGAGAGTTCTTGTATCATATTCTAGGGGAAGTCATAAAAGCTGGAGCTACGACTCTCAATATCCCGGACACTGTCGGATACAATCTTCCTTAT
                                      ttcacttctccctcc  CT-rich tract
                           aatgataaaaattca  TA-rich tract