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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatccttgattggttgctcagttgacccgaaccgtccttccttttcagtcatagtttatcacaggattttgccaaataaattcgtactcaatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC

Basic information

species Zea mays
transcript GRMZM2G053764_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 2
----tcatccttgattggttgctcagttgacccgaaccgt----ccttccttttcagtcatagtttatcacaggattttgccaaataaattcgtactcaatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC-
     |    |||||    |  ||| |    | | | | |    | | | |||||| |  || ||| | |      |  |    ||   ||    ||   ||||| ||||   || || || ||||| ||||| || || || ||  |||| ||||| |||||||||||||| || ||||| ||||| ||||||||||| |||||||| 
ttgtcctgttttgatatccttttcaatatttctgtatcatgtaccttcctttttcaatagtattttttta------tccgtttgatggcttttggct---tttggcaggTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGCTTTATCAACAAGATCTATCACCCA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
tcatc--cttgattggttgctcagttgacccgaaccgtccttccttttcagtcatagtttatcacaggattttgccaaataaattcgtactcaatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC
|  |    |||    |||      |       ||   | ||   || |    | |  ||| |||   |  |||    |     ||  |      ||||| ||||   || || || ||||| ||||| || || || ||  |||| ||||| |||||||||||||| || ||||| || || ||||||||||| ||||||||
ttgttgttttgtcctgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatctgtttgatggct--tttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
















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|12968800|gb|BG265836.1|BG265836
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5895766|gb|AW037012.1|AW037012
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|6022600|gb|AW067412.1|AW067412
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5713918|gb|AI943903.1|AI943903
EST:     GATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5649980|gb|AI920340.1|AI920340
EST:     TCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: TCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|87156694|gb|DY401483.1|DY401483
EST:     GGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|211363205|gb|FL271919.1|FL271919
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT

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: 404

GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1021

GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1200

GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 602

GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtcatagtttatcacaggattttgccaaataaattcgtactcaatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC
                             aaataaatt  TA-rich tract