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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttcattccatgtttagatttctccttaattaattccttcatcttcgtcaactgtcatgctactcactactctgacactcacaatccatctcaacttgttaccctacattatgtatgtatgtatgtttatttgttttattccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG

Basic information

species Zea mays
transcript GRMZM2G164916_T03
intron # 1
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|22490540|gb|BU050463.1|BU050463
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAA                         GGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|71775257|gb|DR973135.1|DR973135
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCG-A                         -------A-AACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|211278361|gb|FL132344.1|FL132344
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCG-A                         -------A-AACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|211404678|gb|FL116464.1|FL116464
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAA                         GGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|211278362|gb|FL132345.1|FL132345
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCG-A                         -------A-AACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|211061080|gb|FL205432.1|FL205432
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAA                         GGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|18965054|gb|BM661366.1|BM661366
EST:     TAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAA                         GGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|211280152|gb|FL132346.1|FL132346
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCG-A                         -------A-AACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
EST: gi|76018661|gb|DT945831.1|DT945831
EST:     TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCG-A                         -------A-AACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA
genomic: TCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGA

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: 45 (upstream exon), 48 (downstream exon)
Score: 64

GGAGGCTCTTTCAGTTCCATCCATCTTCTCCCTCGTGGCTCTCCTTCCTCTCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GGAGGCTCTTTCAGTTCCATCCATCTTCTCCCTCGTGGCTCTCCTTCCTCTCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 47

GGAGGCTCTTTCAGTTCCATCCATCTTCTCCCTCGTGGCTCTCCTTCCTCTCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

GGAGGCTCTTTCAGTTCCATCCATCTTCTCCCTCGTGGCTCTCCTTCCTCTCTCCCGTAGTCCCGCCGACCCCCCGCGCCGGCCAAGGAAATCAAGCGAAgtgagcttca ... tccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttaccctacattatgtatgtatgtatgtttatttgttttattccctgctagGGGCCGCAGAACGCCAGATTTTGATTGTTCCACATCTTCTTTCATCTCTGAGGGGTTTCCCGTCTTCCTCGCCTG
                                   tttgttttattccct  CT-rich tract
                   tatgtatgtatgttta  TA-rich tract