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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctaatttttgcatgctgttgtacacctataccctggctaaacatgaaccagagttgcccatattaagactttttcacctatatgctatatccagtatagattagattgatatttttactaatattatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACACTCACGGAAGCTCTAATTGATCATTTGCAGCCTATTCAG

Basic information

species Zea mays
transcript GRMZM2G177970_T01
intron # 13
splice site 3'
intron type U2

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|32944158|gb|CF048977.1|CF048977
EST:     GAAGAAATCTTCTCTCTATATACCAGATTATCACTGGGAAGACTAAGGAG                         GAAGTTGTTGGTGAGTGCCAACACATGAACTGGGGTA
genomic: GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTA
EST: gi|32930432|gb|CF035244.1|CF035244
EST:     GCAGAAATCTTCTCTCTATATACCAGATTATCACTGGGAAGACTAAGGAG                         GAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTA
genomic: GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTA
EST: gi|71449703|gb|DR830753.1|DR830753
EST:     GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAG                         GAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACA
genomic: GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACA
EST: gi|32930572|gb|CF035384.1|CF035384
EST:     GCAGAAATCTTCTCTCTATATACCAGATTATCACTGGGAAGACTAAGGAG                         GAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGT
genomic: GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGT
EST: gi|78120427|gb|DV538811.1|DV538811
EST:     GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAG                         GAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACA
genomic: GCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACA

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: 143

TATGGAGTTTGACAACCCAGAGAGGCCGGAATGCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACACTCACGGAAGCTCTAATTGATCATTTGCAGCCTATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

TATGGAGTTTGACAACCCAGAGAGGCCGGAATGCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACACTCACGGAAGCTCTAATTGATCATTTGCAGCCTATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

TATGGAGTTTGACAACCCAGAGAGGCCGGAATGCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACACTCACGGAAGCTCTAATTGATCATTTGCAGCCTATTCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 62

TATGGAGTTTGACAACCCAGAGAGGCCGGAATGCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAGgtatctaatt ... tatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACACTCACGGAAGCTCTAATTGATCATTTGCAGCCTATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgctatatccagtatagattagattgatatttttactaatattatttttcagGAAGTTGTTAGTGAGTGCCAACACATGAACTGGGGTACATTCAAGACTACACTCACGGAAGCTCTAATTGATCATTTGCAGCCTATTCAG
                                    tactaat  putative branch site (score: 62)
                                            ttatttttc  CT-rich tract
             agtatagattagattg  TA-rich tract