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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtcaatggcatttggtttgcagtgatttaatttacagccgagaatcatcggttttaccaaacaccaacgcaccacgtacgtgcgcttctgcttctgctgctgctgcag

Basic information

species Zea mays
transcript GRMZM2G152477_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152477_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g13540.1 (Oryza sativa), 5'ss of exon 6
GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtcaat-ggcatttggtttgcagtgatttaatttacagccg---agaatcatcggttttaccaaacaccaacgcaccacgt---acgtgcgcttctgcttctgctgctgctgcag
| ||| ||| |||| ||||||||||| ||||| |||||||||||||||||||| ||||||||||||||||||   ||| | | ||    |||| |  |  ||||  | ||||      ||||  |    | ||  || | | | | | | |  ||   || ||      |||  || ||  || | |||
GTCAATGGCATCGACTTCTACATCAATGGGCACGACCACTGCCTGGAACACATTAGCAGCAGAGACAGgttaacatcatttgacacaaagtttccgct--tttatgtcacagtaatatagaacaaaacatgtttgcata-atcgatgaaacttgtctaacctgaatgcatgca-ctcctattgttacag
















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|37388405|gb|CF631411.1|CF631411
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|148966045|gb|EE016979.2|EE016979
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|78075832|gb|DV504266.1|DV504266
EST:     ACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: ACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|16927228|gb|BM080297.1|BM080297
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|32845008|gb|CD984689.1|CD984689
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGT
EST: gi|149107110|gb|EE189000.2|EE189000
EST:     CTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: CTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|32845140|gb|CD984821.1|CD984821
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTA
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTA
EST: gi|211405855|gb|FK952122.1|FK952122
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|60349280|gb|DN216253.1|DN216253
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|32844554|gb|CD984235.1|CD984235
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGT
EST: gi|50335509|gb|CO530635.1|CO530635
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|78114010|gb|DV532399.1|DV532399
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|32844045|gb|CD983726.1|CD983726
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGT
EST: gi|37393857|gb|CF634195.1|CF634195
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|71430080|gb|DR811130.1|DR811130
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|76012839|gb|DT940009.1|DT940009
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|211405854|gb|FK952121.1|FK952121
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGC-GTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|32835913|gb|CD975591.1|CD975591
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACGTCAGCAGCAGAGACAG                         CCCAATCCAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGT
EST: gi|18162089|gb|BM331928.1|BM331928
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|101387886|gb|EB815958.1|EB815958
EST:     CAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: CAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|110940413|gb|EE160570.1|EE160570
EST:     GAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: GAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|71767916|gb|DR965853.1|DR965853
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|76289548|gb|DV029116.1|DV029116
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|44900102|gb|CK826647.1|CK826647
EST:     TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGTGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
EST: gi|211405853|gb|FK952120.1|FK952120
EST:     TACATCAACCTTCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG                         CCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT
genomic: TACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGT

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: 200

GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGTGCAGAACCCCACCGAAGATGACCTCAAGTTCTTCTACGACGGGCAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 912

GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGTGCAGAACCCCACCGAAGATGACCTCAAGTTCTTCTACGACGGGCAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 923

GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGTGCAGAACCCCACCGAAGATGACCTCAAGTTCTTCTACGACGGGCAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAGgttagtgtca ... gctgctgcagCCCAATCCAGTACTTCACAAGCGGAGGCGGTTCCAAGGCATGGAGAGGAGTGCAGAACCCCACCGAAGATGACCTCAAGTTCTTCTACGACGGGCAAGGC