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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgtggtggttactgtaatactactacttttctctttttccccttatttttatctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG

Basic information

species Zea mays
transcript GRMZM2G305321_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G305321_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 5
gtgcttgtggtggttactgtaatactactacttttctctttttccccttatttttatctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG
|||  | || || ||||       || | ||||| || ||||| |  |      ||| | ||||   |   |||   |||||||| ||||||| ||||||||||| || || ||||||||||| ||||||||||||||||||||||||||| ||| ||||||||||
gtgaatatgatgattac-------ctgcaactttcctgtttttgctatgtccggtat-taatttttttacatatcgaaccagGTGCTGGAAGGACTTGTTTATCTTCACGAGCAAGGTGTCATACATAGAGATATCAAGGGCGCAAATATATTGACTACCAAAGAG

upper sequence: GRMZM2G305321_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------gtgcttgtg-gtggttactgtaatactactacttttctctttttccccttatttttatctgatttcagTTTTTATATGAC--CAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG
               |  |||||| || ||   |    ||||   |  | ||   |  | || || |  || | |   || | ||   ||| |    ||||| |||||||||||||||||  ||||||| || |||||||||||| | || |||||||| || || |||||||  || || |||
ggtggtttggtattagatcttgtgtgtagtgtgtaggttactggaaggtatcatataattccattttaattgttttgattgatttggcataagtttgcagGTTTTGGAAGGTCTTGTTTACTTGCATGAGCAGGGTGTCATTCATCGTGACATCAAGGGTGCCAACATACTGACCACTAAGGAG

upper sequence: GRMZM2G305321_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------gtgcttgtggt---ggttactgtaatactactacttttctctttttccccttatttttatctgatttcagTT-TTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG
                | ||| || |   ||||   || ||   ||           ||| |   ||| || | | |||||    |   |  |||    ||||||||||||||||||||||  |||| || || |||||||||||  | ||||||||||| || || |||||||  || || |||
gttgttgttatttagatccttatgttcttggttgaggtgatcgaacaggagcatggatttacgttttaattgt-tgtgattcgtttgactcgtatttatagGTGTTGGAAGGTCTTGTTTACTTGCACGAGCAGGGTGTCATTCACCGTGATATCAAGGGTGCCAACATACTGACCACGAAGGAG

upper sequence: GRMZM2G305321_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ14289 (Selaginella moellendorffii), 3'ss of exon 5
gtgcttgtggtggttactgtaatactactacttttctctttttccccttatttttatctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG----------------------------------------------------------------------------------------------------------------------------------------------
                                                           || | |    |  ||||   ||||| |||||||| || |  ||||| |||||||||||||| ||||||||||| || ||||| || || || || |  || ||||||                                                                                                                                              
--------------------------------------------------------gtggagtgctaactcgatattcacaggtcttggaaggactggcatatcttcatgaacaaggtgttattcatagagacattaagggggctaacatcctcacgacgaaagaggtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA

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), 49 (downstream exon)
Score: 125

GTATGTGGAGAATGGCTCACTTGCCAATATTATCAAGCCAAACAAATTCGGACCTATTCCTGAATCTTTGGTGGCTCTTTACATTGCTCAGgtgcttgtgg ... ctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 57

GTATGTGGAGAATGGCTCACTTGCCAATATTATCAAGCCAAACAAATTCGGACCTATTCCTGAATCTTTGGTGGCTCTTTACATTGCTCAGgtgcttgtgg ... ctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

GTATGTGGAGAATGGCTCACTTGCCAATATTATCAAGCCAAACAAATTCGGACCTATTCCTGAATCTTTGGTGGCTCTTTACATTGCTCAGgtgcttgtgg ... ctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 160

GTATGTGGAGAATGGCTCACTTGCCAATATTATCAAGCCAAACAAATTCGGACCTATTCCTGAATCTTTGGTGGCTCTTTACATTGCTCAGgtgcttgtgg ... ctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactgtaatactactacttttctctttttccccttatttttatctgatttcagTTTTTATATGACCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGAGTACCAAAGAG
                                           atctgat  putative branch site (score: 160)
               ctacttttctcttttt  CT-rich tract
                                   ttatttttatctgatt  TA-rich tract