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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggagttcatctggttttgcatttatcgtttttttttctctttgatgtggaattccatctttgcttatgatttactacttacctttggatttttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA

Basic information

species Zea mays
transcript GRMZM5G829544_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 4
gtttggagttcatctggttttgcatttat--cgtttttttttctctttgatgtggaattccat-ctttgcttatgatttactacttacctttggatttttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA
|||||  ||| |||    ||||||||| |  | ||| ||||  |   || |||  |    |||  |||  |  |  |  | | || |   ||    | ||| ||||||||||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||| || || |||||||| |||||||||||||| || || |||
gtttgt-gtttatcg---tttgcatttgttgcatttcttttgtttcatgctgtttaccagcatgttttattccttttcgattgctaattgttcctctcttgtttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCGTATTTCAATGGCCGTTCTGCTATA

upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 4
-----------------------gtttggagttcatctggtt--ttgcatttat-----cgtttttttttctctttgatgtggaattccatctttgcttatgatttacta--cttacctttggatttttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA
                        |       |||||||  |  ||   |||||       |    | ||    ||  ||    ||  |||| ||| | ||   | | |   ||    ||   ||  || ||||||||||||||||||||||| | ||||| |||||||| ||||| |||||||| || |||||||| || || ||||||||||||||||||| ||| ||||| |||
gtttgggcttcaactttattctattgcaagaatcatctgtatcgttttttttatgaggatatccaatcttggtatttctgcttgatcacatcattgataattgctaattgtgctccttttccaatcctttcttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA

upper sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g43090.1 (Oryza sativa), 3'ss of exon 5
gtttggagttcatctgg----ttttgcatttatcgttttt-ttttctctttgatgtggaattcc---------atctttgctta----------tgat--ttactactta----ccttt---ggatttttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA
||||||  |||| |||     | |||||   ||| | | | |  | | |||  || |||  |||         || | |||||           ||||  | |||| ||     |||||         ||  |||||||||||||||||||||| | ||||| |||||||| ||||| |||||||| || |||||||| || || ||||||||||||||||||| ||| ||||| |||
gtttgggcttcaactgtattctattgcaagaatcatctgtatcattttttttgtgaggacatccaatcttggtatttctgcttggtcacatcattgataatcactaattgtgctccttttccaatccatttgttgcagTGTTTGGGTGATGATGCACAAGAAAACTAGAAGACTTTCAAAAATGCCAGATGAAGTTAGAGCTGAAATAGGCCCATATTTCAATGACCGTTCAGCTATA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148991050|gb|EE032494.2|EE032494
EST:     TGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAG                         TGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGA
genomic: TGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAGgtttggagtt ... ttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGA
EST: gi|76019085|gb|DT946255.1|DT946255
EST:     TGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAG                         TGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGA
genomic: TGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAGgtttggagtt ... ttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGA

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: 160

AAGTGGACACATGGGTAGCTGCTGCTGGGAAAAATGGCATGCGTCGAGATTGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAGgtttggagtt ... ttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

AAGTGGACACATGGGTAGCTGCTGCTGGGAAAAATGGCATGCGTCGAGATTGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAGgtttggagtt ... ttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 29

AAGTGGACACATGGGTAGCTGCTGCTGGGAAAAATGGCATGCGTCGAGATTGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAGgtttggagtt ... ttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

AAGTGGACACATGGGTAGCTGCTGCTGGGAAAAATGGCATGCGTCGAGATTGGCATGTTCGTGACGAAAACTCTGGACGCACAATCTTGAGAGCTACAAGgtttggagtt ... ttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaattccatctttgcttatgatttactacttacctttggatttttgcttgcagTGTTTGGGTGATGATGAATAAGAACACTAGAAGGCTTTCGAAAATGCCGGACGAAGTTAGGGCCGAGATAGGCCCATATTTCAATGGCCGCTCAGCCATA
                            tacttac  putative branch site (score: 101)
                                          tttttgctt  putative PPT
                 ttatgattta  TA-rich tract