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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatctctcctcggaatatgtggttctagttcactaaaaatgggccttgtcatatttttctagaactggtgctgactggtgtgtgtggttggccttgcag

Basic information

species Zea mays
transcript GRMZM2G108225_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108225_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 5'ss of exon 3
AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatctctcctcggaatatgtggttct--agttcactaaaaatg-ggccttgtcatatttttctagaactggtgctgactggtgtgtgtggttggccttgcag
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AGGACGACACTAGCATTCCTGCCGCGGTGAAGGTGCCGATCCTTAAGGAATTCCATCGGCATATCTACAACCGCGACTGGCATTATTCATgtacggtatcgctccactaaatatgctgttctcaggctgagcaggatggcggcttttttgtgttttgtta-atcggagtttgattggtttg-atg--tgaccttgcag
















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|211235616|gb|FL131352.1|FL131352
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGC
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGC
EST: gi|211235613|gb|FL131349.1|FL131349
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAG
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAG
EST: gi|149098979|gb|EE184992.2|EE184992
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|211062221|gb|FL131346.1|FL131346
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCTACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAAT
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAAT
EST: gi|149089299|gb|EE178514.2|EE178514
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|61119737|gb|DN560698.1|DN560698
EST:     TACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: TACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|148959751|gb|EC905647.2|EC905647
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|74240348|gb|DT648262.1|DT648262
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|149000700|gb|EE037914.2|EE037914
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|148941371|gb|EC886282.2|EC886282
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|211062220|gb|FL131345.1|FL131345
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGG
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGG
EST: gi|85152394|gb|DW587719.1|DW587719
EST:     GGCATTATTCGT                         N
genomic: GGCATTATTCGTgtatgggatc ... ggccttgcag-
EST: gi|85152394|gb|DW587719.1|DW587719
EST:     GGCATTATTCGT                         N
genomic: GGCATTATTCGTgtatgggatc ... ggccttgcag-
EST: gi|148954555|gb|EC899993.2|EC899993
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|211235614|gb|FL131350.1|FL131350
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCTACTGGCATTATTCGT                         GTGGA-CAAATCACT
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACT
EST: gi|149010292|gb|EE042121.2|EE042121
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|211235615|gb|FL131351.1|FL131351
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
EST: gi|148940819|gb|EC885646.2|EC885646
EST:     CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGT                         GTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA
genomic: CCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCA

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), 49 (downstream exon)
Score: 102

AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCACTGCCTTCCTGGAGCTTGGTGAAGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 66

AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCACTGCCTTCCTGGAGCTTGGTGAAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 77

AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCACTGCCTTCCTGGAGCTTGGTGAAGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 97

AGGACGACACTAGCATCCCGACCGAGGTGAAGGTGCCCATCCTCCAGGAATTCTACCGGCACATCTACAACCGCGACTGGCATTATTCGTgtatgggatc ... ggccttgcagGTGGAACAAATCACTACAAAATGCTAATGGATAAGTTTCGCCACGTATCCACTGCCTTCCTGGAGCTTGGTGAAGG