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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatatctgaaacctctgctcacgtgccaagtcaagcttgagaagagtgtaacattgtgaatgcctaaatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG

Basic information

species Zea mays
transcript GRMZM2G133121_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133121_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g10280.3 (Oryza sativa), 3'ss of exon 12
gtttgatatctgaaacctct--------------------gctcacgtgccaagtcaag-cttgagaagagtgtaacattgtgaatgcctaaatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG
||||||| |||||||||  |                    | | || ||| |||||||   ||   |||  || || ||  |  |      ||||||  || | || |||||||| || ||||||||||||||| |||||||  |||||||    ||| ||||||| || || || ||||||||||||||||||||||| |
gtttgatctctgaaacccttccattgacaagttatgaaatgtttacatgctaagtcaaaattttctaaggatgcaaaatgattgactgtcgaattttgtagCTTACAATTGTTTCGGCTCATCGTACACCAGAGAGGATGTACCATTATGCATTATCTACTAAAGAAAGAGGCTTAGAGGTCATAATTGCAGGTGCAGGTG
















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|211118595|gb|FL071335.1|FL071335
EST:     TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAG                         GTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
genomic: TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
EST: gi|211118591|gb|FL071331.1|FL071331
EST:     TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAG                         GTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTWTGATTATGCG
genomic: TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
EST: gi|211118596|gb|FL071336.1|FL071336
EST:     TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAG                         TTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
genomic: TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
EST: gi|29167951|gb|CB411211.1|CB411211
EST:     TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAG                         TTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
genomic: TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
EST: gi|211118592|gb|FL071332.1|FL071332
EST:     TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAG                         GTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
genomic: TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCG
EST: gi|9566322|gb|BE475831.1|BE475831
EST:     TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAG                         TTAACTATTGTTTCTGCACATCGTACACC
genomic: TGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACC

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: 46 (upstream exon), 44 (downstream exon)
Score: 41

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 57

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

TTAGCCCTCGTGTTGCTATTATAATGGGGTCCCAATCTGATCTTCCTGTGATGAAAGATGCTGAGAGGGTTTTGAAAGAGTTCGACATACCTTGTGAGgtttgatatc ... aatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgccaagtcaagcttgagaagagtgtaacattgtgaatgcctaaatttttcagTTAACTATTGTTTCTGCACATCGTACACCAGAGCGGATGTATGATTATGCGAAGTCTGCTAAAGACAGGGGTTTCGAGGTCATAATTGCAGGTGCAGGCG
                                        gcctaaa  putative branch site (score: 80)
                                               tttttc  CT-rich tract
                                           taaatttttca  TA-rich tract