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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgactaataacttgaatgcggtgtactagtagaaatctaagagctaataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC

Basic information

species Zea mays
transcript GRMZM2G155816_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------gtaactgactaataacttgaatgcggtgtactagtagaaatctaagagctaataatgtcta-gtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
                                                                              ||   ||  ||||   ||  |     |   |||      || | | |  |||   | |  |  | ||    || || | |    | || |     |||||||| |||||||||||||||| || ||   |||| |||||||| ||||||||||||||||||| ||||||||| ||||||||| | |||||||| || ||   
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacg---attttaaatttaactttatgaatatattgattaacatatatatg-gttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGC---AGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT

upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
---gtaactgactaata-acttgaatgcggtgtac-tagtagaaatctaagagctaataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
   | ||   |   ||| |||||   ||  || |  |  ||  | |    ||| |  |  |  |  |   |    || || |||| ||| |      |  |||||  ||| ||||||||  |    | ||||||| | |||||||||||||||||||| ||||||| ||| ||||| || || ||  |||| || || || ||   
atggaaagaaagacatagacttgttagccttgaaggttataatacttcttgagttttttgtagcatgaactagttaacatatgttgatgct---tcttttcagATAAGTGTAGGATTGGATC---AGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC

upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
----gtaactgactaata-acttgaatgcggtgtac-tagtagaaatctaagagctaataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
       |  ||| || | | |||    |  || |  |  ||    |    ||| |  |  |  |  |   |    || || | ||   ||||     | ||||||  ||| ||||||||| |    | ||||||| | |||||||||||||||||||||||||||| ||||||||| || || ||  |||| ||||| || ||   
tggaaagaaagacaaaaatatttgttaactatgaaggttataatgcttcttgagttt-ttgtaacatgaactagttaacatatatt---ggtgcttctttgcagATAAGTGTAGGATTGGGTC---AGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC

upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaactgactaataacttgaatgcggtgtact--agtagaaatctaagagcta-ataatgtctagtgt-ttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
 |   ||  |||  |  |  ||    | ||||  ||   | |  ||| |  |  ||  | || | | | || | || |  | ||  || ||   |   | |||    ||||| || ||| |   ||  |||||  |||||||||||||||| ||||||||||||| ||| || || || ||||| ||||| |||||||||||   
-tgtgtgtttaaatatatatatata-tatacttaagactataattaacaattgtattttttcaattatatttataacaaattttgttgttgtgtgtatgtagAGAAATGCAGAATCGGGTC---GGGTCCTCAAAACGAGTGGTATTTCTTTAGCCACAAGGACAAGAAATATCCGACTGGGACCCGAACGAACCGGGCGACAGC

upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0085g01210.t01 (Vitis vinifera), 3'ss of exon 1
-gtaactgactaataa--cttgaatgcggtgtactagtagaaatctaagagcta--ataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
  |||         ||  |   || ||    |   ||| || ||    |   ||   || ||   | | |||||   | | ||    |||| | |    ||||||   ||| | |||||  |    |   ||||| |||||||||||||||||||||||||||| | ||| ||||| || || || ||||| ||||| || ||   
actaatcagtccgcaatacccaaaagcaagattaaagttgatattattgcagtacggtattgggaaatttttcatg-tttttggatttggttggca--tgcagATAAATGCCGAATTGGATC---AGGCTCTCAGAACGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATACCCAACTGGAACTCGAACAAACCGAGCAACCAT

upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
----------------gtaactgactaataacttgaatgcgg---tgtactagtagaaatctaagagctaataatgtctagtgtttcacaat-atgtgttcatggtg---gacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
                  ||    || ||  |   ||         || ||  | ||| |||  | | |   |||||||  | | ||||    ||   |  || | |   | |   | |||| |||||| | |||||  | |||||||   || |||||||||| |||||||||||||| |||| ||| ||||| || |||||| | |||||| | || ||   
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctt-tggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGC---AGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: GRMZM2G155816_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
--------------------gtaactgactaataacttgaatgcggtgtactagtagaaatctaagagctaataatgtctagtgtttcacaat-atgtgttcatggtg---gacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC---
                    |   || | |         ||      || ||  | ||| |||  | | |   |||||||  | | ||||    ||   |  || | |   | |   | |||| |||||| | |||||  | |||||||   || |||||||||| |||||||||||||| |||| ||| ||||| || |||||| | |||||| | || ||   
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctt-tggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGC---AGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

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|211508051|gb|FL351572.1|FL351572
EST:     TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAG                         ATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
genomic: TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAGgtaactgact ... acgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
EST: gi|211022949|gb|FL309675.1|FL309675
EST:     TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAG                         ATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
genomic: TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAGgtaactgact ... acgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
EST: gi|211088239|gb|FL309315.1|FL309315
EST:     TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAG                         ATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
genomic: TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAGgtaactgact ... acgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
EST: gi|211206023|gb|FL351337.1|FL351337
EST:     TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAG                         ATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA
genomic: TGTCATAAGGGAGGTGGACCTCAACAAGCTTGAACCATGGGACCTCAAAGgtaactgact ... acgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagctaataatgtctagtgtttcacaatatgtgttcatggtggacgatcgcagATCGGTGCAGGATTGGGACGGCGGAGCCTCAGGACGAGTGGTATTTCTTCAGCCACAAGGACAGGAAGTACCCTACGGGGACGCGAACCAACCGGGCGAC
   agctaat  putative branch site (score: 3)
      taataatgt  TA-rich tract