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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctacaaccgtttgcttcttgcttcattttttttagttcatgtcttggcttctctgcctggtatcagtaataccagaatttaggttcctagcttgtagcttcccccttccggagcattttacatttcggagttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG

Basic information

species Zea mays
transcript GRMZM2G010044_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ16664 (Selaginella moellendorffii), 3'ss of exon 1
gtacgctacaaccgtttgcttcttgcttcattttttttagttcatgtcttggcttctctgcctggtatcagtaataccagaatttaggttcctagcttgtagcttcccccttccggagcattttacatttcggagttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG
                                                                                    || |||    |  | |    | |    | |||    | | ||    |||| |||  ||||||| ||||| |||||||| || || |||||| | || |||||||||||||| |||||| | || ||||||
-----------------------------------------------------------------------------------gtacgtttgcggtgtttg---tacgtgattcggtcgctctaac---ccggatttga-tgcagGCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAG
















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|31355882|gb|CD440239.1|CD440239
EST:     AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGG                         GCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
EST: gi|71772889|gb|DR970812.1|DR970812
EST:     AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGG                         GCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
EST: gi|211187638|gb|FL072207.1|FL072207
EST:     AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGG                         GCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAAGC
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
EST: gi|211185238|gb|FL072192.1|FL072192
EST:     AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGG                         GCTAATCCGGACTACA
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACA
EST: gi|31354069|gb|CD438426.1|CD438426
EST:     AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGG                         GCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
EST: gi|76012112|gb|DT939282.1|DT939282
EST:     AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGG                         GCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC
genomic: AGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGC

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: 39 (upstream exon), 40 (downstream exon)
Score: 23

CGACGGCCGTGCCAAACGCAACGTCGACATCCTCAGGGACTTCTGTGCGGAGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

CGACGGCCGTGCCAAACGCAACGTCGACATCCTCAGGGACTTCTGTGCGGAGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 30

CGACGGCCGTGCCAAACGCAACGTCGACATCCTCAGGGACTTCTGTGCGGAGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 26

CGACGGCCGTGCCAAACGCAACGTCGACATCCTCAGGGACTTCTGTGCGGAGCAGAACATCAAGTACTTCTATGACATCAAGGACCTCAGCGATTTCAGGgtacgctaca ... ttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagcttgtagcttcccccttccggagcattttacatttcggagttgtctgcagGCTAATCCGGACTACAAAGGCGTCTGCCACATCGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG
                             attttacattt  TA-rich tract