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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttatattgtgcttccttttagttgcttcaatgacatcctttgcataattcagaatatcagtgtgatgaaactggtcatcccctacattccatagacatcagactgaaacttgtttggttggtcatcgtctgattgtggcatttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 23
gtaacttatattgtgcttccttttagttgcttcaatgacatcctttgcataattcagaatatcagtgtgatgaaactggtcatcccctacattccatagacatcagactgaaacttgtttggttggtcatcgtctgattgtggcatttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC
                                           ||| | | ||    ||   || |   ||  ||  |  |  | | || ||    |   |  ||    |||| ||||||| |||||     ||| |||||||  ||| ||  |||||| || |||||||||||||||||| |  | ||||||||||| ||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||||
-------------------------------------------tttcctttatctttaagg-caatacaattcaatcgtcctgcacataaatcaagtgatc--caattggaaagttgtttg-ttggt-----tcttattgtggtctttgca--gGAGGTGTCATTTATGCTTCCACCTCTTTTGGGCTTGCTGCTTGAGTGTGCCAAGAAAACAGACCAGACTGTTGTTTCAATTGCTCTTGGAGCTTTAGTTC
















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: 49 (upstream exon), 49 (downstream exon)
Score: 254

TGGGAGGGATGGACTTTCTTCTTCTGGGGATGATTGGCTTCGTGATACTAGCATTCATTCACTGCAGTTAATCTGCAACCTTTTCAATACATTCTATAAGgtaacttata ... atttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TGGGAGGGATGGACTTTCTTCTTCTGGGGATGATTGGCTTCGTGATACTAGCATTCATTCACTGCAGTTAATCTGCAACCTTTTCAATACATTCTATAAGgtaacttata ... atttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

TGGGAGGGATGGACTTTCTTCTTCTGGGGATGATTGGCTTCGTGATACTAGCATTCATTCACTGCAGTTAATCTGCAACCTTTTCAATACATTCTATAAGgtaacttata ... atttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC


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

TGGGAGGGATGGACTTTCTTCTTCTGGGGATGATTGGCTTCGTGATACTAGCATTCATTCACTGCAGTTAATCTGCAACCTTTTCAATACATTCTATAAGgtaacttata ... atttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcagactgaaacttgtttggttggtcatcgtctgattgtggcatttacacagGAGGTATCCTTTATGCTTCCACCTCTTCTCAGTTTGCTGCTTGAATGTGCGAAAAAAACAGACCAAACTGTCGTTTCAATTGCTCTTGGCGCTTTAGTTC
                                gtctgat  putative branch site (score: 258)
                                             atttaca  TA-rich tract