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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCAGGGATGCAGCAACAGGGCGAGGCGTAATGTATGCTACCGAGGCCCTACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgatagtttattcacatatgtccatcgaatgtacttttataagatgataaaaggataaccacatgttccctatagcaggttacctactgaaatattagttttttttaaaaaaactctatatttgtatatttgctatcgtgtcagtatgcaatatatatggtttaatatgtaaaccttgcag

Basic information

species Zea mays
transcript GRMZM2G427097_T01
intron # 5
splice site 5'
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|20300129|gb|BQ163072.1|BQ163072
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|211012376|gb|FL318441.1|FL318441
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|60395163|gb|DN228032.1|DN228032
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|18384249|gb|BM417448.1|BM417448
EST:     ACTCGCCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: ACTCG-CTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|18963184|gb|BM660288.1|BM660288
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAG
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAG
EST: gi|211264916|gb|FL208732.1|FL208732
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCMATGTTGGTTCATGGGCTGCTCGACT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACT
EST: gi|18655200|gb|BM500005.1|BM500005
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|18383740|gb|BM416940.1|BM416940
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|18655120|gb|BM499925.1|BM499925
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|32825912|gb|CD965590.1|CD965590
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTATTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|87152706|gb|DY397495.1|DY397495
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|32944867|gb|CF049686.1|CF049686
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
EST: gi|22490092|gb|BU050015.1|BU050015
EST:     TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAA                         GGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT
genomic: TACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGT

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), 47 (downstream exon)
Score: 68

GGGCAGGGATGCAGCAACAGGGCGAGGCGTAATGTATGCTACCGAGGCCCTACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGTGGTAAGATTATTGCAATTGGGGATGTGACAGGTTCAATTAGAAACACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 510

GGGCAGGGATGCAGCAACAGGGCGAGGCGTAATGTATGCTACCGAGGCCCTACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGTGGTAAGATTATTGCAATTGGGGATGTGACAGGTTCAATTAGAAACACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

GGGCAGGGATGCAGCAACAGGGCGAGGCGTAATGTATGCTACCGAGGCCCTACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGTGGTAAGATTATTGCAATTGGGGATGTGACAGGTTCAATTAGAAACACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

GGGCAGGGATGCAGCAACAGGGCGAGGCGTAATGTATGCTACCGAGGCCCTACTCGCTGAATATGGAAAATGCATTTCTGGATCAACTTTTGTGATCCAAgtgagtgata ... aaccttgcagGGTTTTGGCAATGTTGGTTCATGGGCTGCTCGACTTATTCACGAGAAAGGTGGTAAGATTATTGCAATTGGGGATGTGACAGGTTCAATTAGAAACACGG