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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggctcttgaaaacagcaataaagaactaaattcaaatccaaaaccagtttgaacctactttctcttgctgttgatccaatacctcgttttcttggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATATTACATTAACCATTAATTCCTGGCGTTC

Basic information

species Zea mays
transcript GRMZM2G168249_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168249_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os06g08790.1 (Oryza sativa), 3'ss of exon 15
gtcggctcttgaaaacagcaataaagaactaaattcaaatccaaaaccagtttgaacctactttctcttgctg--ttgatccaatacctcgttttcttggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATA-TTACATTAACCATTAATTCCTGGCGTTC
          |   | | |  |     | |  |     ||  |||   | | || ||||  ||| || ||      ||  |  ||   |  ||||||||  || |||||||||||| || |||||||| ||||||||||||||| |||| ||| | ||||||||| ||||| ||| | | || ||       |   ||||  || || 
-------tgagcggagaacttttggttaatctagctggatgaaaacttaatatgcacctcttttatcatgtaaaactgtactgatgattatttttcttgtctggcagTGACGATGTAACTTTTGCCCTGAAGGAATCCCCAGATATTCCATGGTTGTCCAAGTACCTGTGAAGTTTACACTTGCAGCGGTTGTACTTTCCCAGCATT-
















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|5901140|gb|AW042240.1|AW042240
EST:     GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCGAG                         TGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
EST: gi|15100644|gb|BI396435.1|BI396435
EST:     GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCGAG                         TGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
EST: gi|5608069|gb|AI901736.1|AI901736
EST:     GAAAAGGGTAGTAAGCCCAAGTTGCAGAAGGTTCAGCTTAACTATCCAAG                         TGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
EST: gi|111190712|gb|EE288848.1|EE288848
EST:     GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAG                         TGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
EST: gi|32908909|gb|CF013722.1|CF013722
EST:     GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAG                         TGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATC

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: 87

TTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATATTACATTAACCATTAATTCCTGGCGTTC


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 59

TTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATATTACATTAACCATTAATTCCTGGCGTTC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 77

TTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATATTACATTAACCATTAATTCCTGGCGTTC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 58

TTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTAGTAAGCACAAGTTGCAGAAGGTTCAGCTTAACTATCCAAGgtcggctctt ... tggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATATTACATTAACCATTAATTCCTGGCGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaacctactttctcttgctgttgatccaatacctcgttttcttggttgacagTGACGATGTGACATTTGCCCTCAAGGAATCCCCAGATCTTCCTTGGCTATCCAAGTACTTGTGAGGTTCATATTACATTAACCATTAATTCCTGGCGTTC
                     tgttgat  putative branch site (score: 58)
                                tacctcgttttctt  putative PPT
                                       ttttctt  TA-rich tract