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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtccccaaccccatccaccgaaatgcagctccactaccctggcgctaatgcattagtcgggcggcattcgatgattcttctttagtctcaattgcccactcagctcggtcctatgcgccggactttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGGACAACGAGTTCAACTGGGACGGCCATGACTCGCAGTCTGTGGCCGAGTC

Basic information

species Zea mays
transcript GRMZM2G025231_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 2
gtgggtgtccccaaccccatccaccgaaatgcagctccactaccctggcgctaatgcattagtcgggcggcattcgatgattcttctttagtctcaattgcccactcagctcggtcctatgcgccggactttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGGACAACGAGTTCAACTG---GGACGGCCATGACTCGCAGTCTGTGGCCGAGTC
                        | |    || |  || | ||     | |     ||| | |   |  |   |       | |  ||   | ||||||| |||||   |||  |||   ||           ||||||| |||   |||||| |||| ||||||||||||||||| || ||||||||||| ||||||||||||||   |||| |  ||||||||||||  || || ||   
-----------------------gcaagtcacacccgcaatgccgaattggtggca-atttgccccccccctcccccccccgcctagttc-ccccaattgctcactcgattcgcccctgatcgata--------ttgcagGTTGCGCTCGTGTGCCCGGGGACGAGGAGGAGGACGGTGTGGATGACCTGGAGAACGAGTTCAACTGGAGGGACAGGAATGACTCGCAGTACGTCGCGGA---
















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|149001186|gb|EE038454.2|EE038454
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211344801|gb|FL219951.1|FL219951
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAAGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211344804|gb|FL219954.1|FL219954
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|71309263|gb|DR790918.1|DR790918
EST:     GCACGCAAAACTGCCCCCCAGTGCAAGACTCGATACAAGCGCCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTG
genomic: GCACGCAGAACTGCCCCC-AGTGCAAGACTCGATACAAGCGCC-TCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTG
EST: gi|211344807|gb|FL219957.1|FL219957
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211342416|gb|FL219947.1|FL219947
EST:     GGCACGCAGAACTTGCCCCCCGTGCAAGACTCGATACAAGCCCCTCAAGG                         GCTGCCCAGCGTGTGA
genomic: GGCACGCAGAACT-GCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCC-AGCGTGTGA
EST: gi|211344805|gb|FL219955.1|FL219955
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCTATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211342409|gb|FL219940.1|FL219940
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGG
EST: gi|211342413|gb|FL219944.1|FL219944
EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGG                         GCTGCCAGCGTGTGACCGGTGACGAGGAGGGAG-ACGGCGTCNATGACCTG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGG-AGGACGGCGTCGATGACCTG

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 252

GAGTGCGCCTTCCCCGTCTGCCGGGACTGCTACGAATACGAGCGCCGGGAGGGCACGCAGAACTGCCCCCAGTGCAAGACTCGATACAAGCGCCTCAAGGgtgggtgtcc ... ttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGGACAACGAGTTCAACTGGGACGGCCATGACTCGCAGTCTGTGGCCGAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttagtctcaattgcccactcagctcggtcctatgcgccggactttgtttgcagGCTGCCAGCGTGTGACCGGTGACGAGGAGGAGGACGGCGTCGATGACCTGGACAACGAGTTCAACTGGGACGGCCATGACTCGCAGTCTGTGGCCGAGTC
                                           ctttgttt  CT-rich tract
                                            tttgttt  TA-rich tract