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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactag

Basic information

species Zea mays
transcript GRMZM2G116151_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 2
CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgccttctctgga----------atttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactag
 |||||||| ||||||||||| ||||||||||||||||||||||| || |||||||||||| ||||||  |||||||| || || || |||||||| ||||||       ||  || |||          ||||  |  | |||   ||| ||| ||||||   ||  ||| |||| || |||| ||
TAGAAAGCTGGGAAAGGGAGGATTTGGGCAAGTATATGTTGGTCGGCGTATTTCCTCTCCTGGTGTTACCGACAGGACACCTGGAGCAAATGCTTTGGAGgtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 2
CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgt---------ctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgtttttt-ttcatactag
 || ||| | ||||||||||| ||||||||||| |||||||| |||||  | ||  ||   | |   |||||| | ||  | ||  |    ||| | |||||          |||||   ||   |    | || |  |||   |  || |   | |   | ||||    | |  | || ||  |||
AAGGAAGTTGGGAAAGGGAGGATTTGGGCAAGTGTATGTTGGCCGTCGTGTGTCTCCTATAAATCCAAGTGACCGAACTACTGGCCCTGGGGCTCTGGAGgtatattttggttttattttttgattattgtgttgatctgtttcttttctttttttctgaaacatatctatctcctattgattttag

upper sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 2
---------CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGC-CCGGTGCGAATGCTTTAGAGgtctttatgccttctctggaatttttaattgtaatt-catcgtagctgcattagcataaacgttttttttcatactag----------------------------------------------------------
          || || |||||||||||||| ||||| ||||||||||||||||||||         ||  |||| | | | |||  ||| | ||| |  | ||| | |||||  |      | ||||      || |  |    |    |||||       |||     | | || |  | ||  |||                                                          
CAAGATTGAGAGGAAACTTGGAAAGGGAGGCTTTGGTCAAGTATATGTTGGTCGTCG---------TCTCAGTGGTGG-GGCAGAGCGCACTGGTCCACAGGCTGTCGAGgtactc---tttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattat-ttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcag

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|30306558|gb|CD001231.1|CD001231
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|101387539|gb|EB815784.1|EB815784
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|211200248|gb|FK978072.1|FK978072
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGTGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|211200247|gb|FK978071.1|FK978071
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|149078987|gb|EE167841.2|EE167841
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|30031898|gb|CB833749.1|CB833749
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 124

CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 34

CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 36

CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA


Block sizes: 28 (upstream exon), 46 (downstream exon)
Score: 53

CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA