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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA

Basic information

species Zea mays
transcript GRMZM2G128995_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA
               | | |   ||         | | |       |||| |  |||  | | |||| |  ||||||  ||| |   ||| |  ||     |  |||| ||  || |||| |  ||   ||        ||||||||||||   |  |  ||| |   |||||||| ||||||||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| |||||| ||||||| |||||||| |||
-------------gtagattgcatgccactgagtttttg-------gctttaagcca--attctttcttgttttatttcaaaggactcagaaatgcgagggt--atggtttcatc-ttttgttagtcaact--------ctaattagtttgttttccttctgtat---agCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA

upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 5
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA
                                                                            ||| || |  |      |    | |   ||| |||  | || | ||  ||    |||| ||  || | |    || ||| ||    |||   |||||||| || ||||||||||||||  |||||||||| |||||||| || || || ||| || |    || ||||||||||||||||||||||| || || 
---------------------------------------------------------------------------gtgtgaatgttatt---tattgaacaatcatgactttttaatataataagta---tttctta-gctgactttaatgacctatttgcctgttttagCTTAGCTGTCCGTGATCTTTCCAACTTGGTAAAACCTGAGGATATTATAACTTCAGAAAATTTAACCACCCTTCTTGCAATTGTTCCCAAGTATTCACAG

upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA
                                                                      || ||   |    | ||   |   | || |   |   |       ||||||| |  ||   || || | || ||      | ||| ||    ||    ||| |||| ||||||||||||||||| || ||||| || ||||| || ||  |||| |||||| | ||||||||||||||||||||||||||||| || || 
----------------------------------------------------------------------gtataccttggttgaaatctgtttgtaggacaaacaag-------attttatttactgtgatttcttttctgatc-----gacctctttgcttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGCCTCAGAACATTTAGTGACACTTCTTGCAATTGTTCCCAAGTATTCTCAG

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|32907249|gb|CF012062.1|CF012062
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|19351863|gb|BM896395.1|BM896395
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|60358961|gb|DN225934.1|DN225934
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|22491457|gb|BU051380.1|BU051380
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|67013699|gb|CO442448.1|CO442448
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC

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: 124

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 218

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAA
                      tactaat  putative branch site (score: 218)
                                     ccttttatt  putative PPT
                    tatactaattagttt  TA-rich tract