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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA

Basic information

species Zea mays
transcript GRMZM2G128995_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA
               | | |   ||         | | |       |||| |  |||  | | |||| |  ||||||  ||| |   ||| |  ||     |  |||| ||  || |||| |  ||   ||        ||||||||||||   |  |  ||| |   |||||||| ||||||||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| |||||| ||||||| |||||||| |||     
-------------gtagattgcatgccactgagtttttg-------gctttaagcca--attctttcttgttttatttcaaaggactcagaaatgcgagggt--atggtttcatc-ttttgttagtcaact--------ctaattagtttgttttccttctgtat---agCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA-----

upper sequence: GRMZM2G128995_T05 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 5
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA
                                                                            ||| || |  |      |    | |   ||| |||  | || | ||  ||    |||| ||  || | |    || ||| ||    |||   |||||||| || ||||||||||||||  |||||||||| |||||||| || || || ||| || |    || ||||||||||||||||||||||| || ||      
---------------------------------------------------------------------------gtgtgaatgttattt---attgaacaatcatgactttttaatataataagta---tttctta-gctgactttaatgacctatttgcctgttttagCTTAGCTGTCCGTGATCTTTCCAACTTGGTAAAACCTGAGGATATTATAACTTCAGAAAATTTAACCACCCTTCTTGCAATTGTTCCCAAGTATTCACAG-----

upper sequence: GRMZM2G128995_T05 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattgcgctgacatactttgtgtgttcagactctagaggaagtgcttgattccaggactttttccttgtttattgtaaaaggaacaggagagcagaaatgaatggcttactcattttatctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA
                                                                      || ||   |    | ||   |   | || |   |   |       ||||||| |  ||   || || | || ||      | ||| ||    ||    ||| |||| ||||||||||||||||| || ||||| || ||||| || ||  |||| |||||| | ||||||||||||||||||||||||||||| || ||      
----------------------------------------------------------------------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|67018576|gb|CO447325.1|CO447325
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|71427970|gb|DR809020.1|DR809020
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|211413494|gb|FL407160.1|FL407160
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGTAGCAAAGTGGGAG                         CTTAGCGGGTTCGTGATCTTTCCCATCTGGTAAAACCCGGAGGATATGATC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G--TTCGTGATCTTTCCAATCTGGTAAAACC-GGAGGATATGATC
EST: gi|211452191|gb|FL398498.1|FL398498
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|149010225|gb|EE042044.2|EE042044
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|19351525|gb|BM896057.1|BM896057
EST:     AATAATGCAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|31348626|gb|CD432983.1|CD432983
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|149000734|gb|EE037952.2|EE037952
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|148954149|gb|EC899548.2|EC899548
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGG
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGG
EST: gi|67013699|gb|CO442448.1|CO442448
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGCTTAG                     
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGT-GG-G---AGgtaaattgcg ... gaaagc
EST: gi|22491457|gb|BU051380.1|BU051380
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|211319940|gb|FL427662.1|FL427662
EST:     ATAATGTAAGGAGCCNAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGGTTCGTGATCTTTCCCATCTGGTAAAACCGGGAGGATATGATC
genomic: ATAATGTAAGGAGCC-AGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G--TTCGTGATCTTTCCAATCTGGTAAAACCGG-AGGATATGATC
EST: gi|87153287|gb|DY398076.1|DY398076
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|6095541|gb|AW120208.1|AW120208
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|148968978|gb|EE019672.2|EE019672
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|148963815|gb|EE014912.2|EE014912
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|149098811|gb|EE184822.2|EE184822
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G-G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|211532950|gb|FL381081.1|FL381081
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGCCCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGGAGGATATGAT
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G---G-TTCGTGATCTTTCCAATCTGGTAAAACCGG-AGGATATGAT
EST: gi|60358961|gb|DN225934.1|DN225934
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGCTTAG                     
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGT-GG-G---AGgtaaattgcg ... gaaagc
EST: gi|211057980|gb|FL426570.1|FL426570
EST:     AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAG                         CTTAGNCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCA
genomic: AATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagC---G--G-TTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCA

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: 53

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GTTCGAGCATCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGGAAGCAAAGTGGGAGgtaaattgcg ... gaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgttgcctttcctatactaattagtttggccttttattgtgtgaaagcttagCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTCGTGACACTTCTTGCAATTGTTCCCAAGTACTCCCAAAAAGA
                 tactaat  putative branch site (score: 56)
               tatactaattagttt  TA-rich tract