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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctaaaatgaattttaattttggacagagggagtatttatgatggcaagatattctggcaataagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG

Basic information

species Zea mays
transcript GRMZM2G078576_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 15
----------------------------atctaaaatga----attttaatt-ttggacagagggagtatttatgatggc---aagatattctggcaataagattgactg-----acaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
                               | |||||       ||| ||  ||| |||         | | |||   |   || |||||||||      |||||| ||     ||||| ||   |||  | |||| ||||||||||| ||||| ||||||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| ||||| ||
gtgatgcttataatacttagaaactgctgctttaaatggcagttctttgatgattgcacattttcttgttctttgagcacttgaaaatattctggtgtccggattgattggcttgacaatatataatgatctgtttt-cagATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 15
atctaaaatg-aattttaattttggacagagggagtatttatgatg-gcaagatattctggcaa--taagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
   ||| ||| || | || |||| ||     ||  |  ||    || | || |   |  ||     |  |  |   |   |     || |   || ||| |||||||||||||||  |||| || |||||||| ||||| || || || ||||| || |||||||||||||  ||||  || || || || ||  |
--gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccattaggtggattttgtcttgtttctatgaggctgtatcttgtttgtcagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTGCTATCCCGTTG

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 14
atctaaaatg-aattttaattttggacagagggagtatttatgatg-gcaagatattctggcaataagattgactga---caatgta-ctttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
   ||| ||| || | || |||| ||     ||  |  ||    || | || |   |  ||        ||| || |   | |||   || |   || ||| |||||||||||||||  |||| || |||||||| ||||| || || || ||||| || |||||||||||||  ||||  || || || || |   |
--gtaagatggaaatatattttttgatttgtggtttgcttccagtgtggaataccattaggtggattatttgtcttatttctatgaggctgtatcttgtttgtcagATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTTCTATCCCATTG

upper sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 15
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 15
atctaaaatgaattttaattttggacagagggagtatttatgatggcaagatatt--ctggcaa--taagattgactgacaatgtactttgaatt---atttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
   ||||| | | ||   | |||  ||     |||  ||   ||      || ||  |||  |   || | |  ||| |  | ||| | | ||||    |||  ||||||||||| || || || || |||||||| ||||| ||||| || ||||| ||||||||||| ||||  ||||  || || || || ||  |
--gtaaaaggcaattggttgttgagcaattacagttgttccaattaatgaatcttatctgaaaggttatgttccacttatcacgtaatataaatttccgtttgacagATGTTTACACAATTACGCTTCACATATGAACAAGAGAGCCATCCAGAGGAGTTCTTTATCCCCTATGTGTGGCAGCTAGTTCTATCCCGCTG

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|87155515|gb|DY400304.1|DY400304
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGTGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|78111274|gb|DV529671.1|DV529671
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|24766669|gb|CA401816.1|CA401816
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCCCCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|166692487|gb|EG166994.1|EG166994
EST:     ATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: ATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|22472877|gb|BU037357.1|BU037357
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGTGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|149083574|gb|EE172908.2|EE172908
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|37376751|gb|CF624930.1|CF624930
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|148945634|gb|EC890893.2|EC890893
EST:     TTGAAGTCATCAATAAAACTTCCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTATTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
EST: gi|166698538|gb|EG154852.1|EG154852
EST:     TGAAGTCATCAAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCC
genomic: TGAAGTCATC-AATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCC
EST: gi|93282383|gb|EB674647.1|EB674647
EST:     TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAG                         ATGTTTATTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA
genomic: TTGAAGTCATCAATAAAACTTGCCGTTCATGGCGCGGAGAAGGGATGAAGgttttagttt ... tatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagatattctggcaataagattgactgacaatgtactttgaattatttttcagATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGG
                        gactgac  putative branch site (score: 2)
                                            ttatttttc  putative PPT
                               aatgtactttgaatta  TA-rich tract