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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcacagtgctcctggactacatttcacctgtgcccaatacttgctggtagcagcaatgcctgatcattagaaattgtgtttgcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT

Basic information

species Zea mays
transcript GRMZM2G055607_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055607_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g44960.2 (Oryza sativa), 3'ss of exon 2
gtatagcacagtgctcctggactacatttcacctgtgcccaatacttgctggtagcagcaatgcctgatcattagaaattgtgtttgcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT
          || || |  || |  | ||    | |  |  |||    ||| ||||| ||||   |||||||        || || |     |||||| || ||||||||||| |||||||||||||||||  |||  || || ||  |  | || ||| |||| || | |||||| ||||||||||||||  |||
----------gtactgcatgattctagttt-tgtatctctgatat---ctgatagcaacaatatttgatcata-------gttttcgtattcgcagCATCCATATTCACTTAAAAGTTCCAAGGGAGCACCGTTTCCACCGCGACCGATTCTTGTCTTCCTCATTGCAATATTTGGATTCTATGTATGCTACATCT
















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|71431673|gb|DR812723.1|DR812723
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|211383959|gb|FL013551.1|FL013551
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|31441050|gb|CD510481.1|CD510481
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|76911991|gb|DV164525.1|DV164525
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|71448567|gb|DR829617.1|DR829617
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|211383960|gb|FL013552.1|FL013552
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|88755485|gb|DY539626.1|DY539626
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|50329390|gb|CO524516.1|CO524516
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|71437590|gb|DR818640.1|DR818640
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|211132575|gb|FL461421.1|FL461421
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|28987385|gb|CB351608.1|CB351608
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|211383961|gb|FL013553.1|FL013553
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|71305861|gb|DR789056.1|DR789056
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|91871874|gb|EB401831.1|EB401831
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|74241101|gb|DT649015.1|DT649015
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|211383958|gb|FL013550.1|FL013550
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
EST: gi|50330184|gb|CO525310.1|CO525310
EST:     AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATG                         CACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA
genomic: AGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 62

TTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 39

TTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

TTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 520

TTCTGATGCCAATTAGGACTAAACATGCTTCCTCGCTGCGCTCAAGTGGGAGAACAAGAAATCAGCCTAGACACTAGTCATCTGCTGCAAGCAGAAAATGgtatagcaca ... gcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacttgctggtagcagcaatgcctgatcattagaaattgtgtttgcgcctgcagCACCCTTATTCACTTAAGAGTTCCAAGGGAGCACCAATTCTGCCACGGCCAGTCTTCGTTTTCTTCATCGCGACATTTGGTTTCTATGTATGCTATCTCT
                     gcctgat  putative branch site (score: 520)
                             attagaaatt  TA-rich tract