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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaactaccatcctttttccatgcttctgctgctgatttcctttgttcgtcaatatatgataataacctgtgagtgttttttttacttctgttgcggtgcatattcag

Basic information

species Zea mays
transcript GRMZM2G097768_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097768_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g50280.1 (Oryza sativa), 5'ss of exon 3
TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaactaccatcctttttccatgcttctgctgctgatttcctttgttcgtcaatatatgataataacctgtgagtgttttttttacttctgttgcggtgcatattcag
|||||||||||||| || ||||| ||||| |||||||||||||| ||||| |||||||| ||||| |         | | |  || |     ||| | |   ||   ||  | || | |   |||  |||| | || |            |||||||     | |  ||| |||
TCTCTCATGATCGCGGCAATTCCTAACATTATTGGGTGGCTCGCAATATCTTTTGCAAAGgtaaggtt--------ttcatgctcgag----ctgttaccagttagtttgatccgccca---atgccaatagcttgcgca----------acttctgaaattg-gtttatccag

upper sequence: GRMZM2G097768_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G08070.1 (Glycine max), 5'ss of exon 4
TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaactaccatcctttttccatgcttctgctgctgatttcctttgttcgtcaatatatgataataacctgtgagtgtt-----ttttttacttctgttgcggtgca--tattcag----------------------------------------------------------
||| | ||||| ||  | |||||||| || ||||| ||||| || || |||||||||||||||||||  | |    |   | ||  ||  |||  |   | |||| |         || ||  || || |    ||||  | |      ||| ||  || |       ||||  |||| ||                                                          
TCTTTGATGATTGCATCCATTCCAAATATTATTGGTTGGCTGGCTATCTCATTTGCAAAAgtaagtttgaatgattttagtattttat-tttcctccattcatttacccaaaattacattaattggtatttcaatgtggttctggataatttattgtttatccaaacatgcaattatttagtaaatatatttggtcgtgattctgagcttgtcttattgacatgttcttcaattttcag

upper sequence: GRMZM2G097768_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT1G19450.1 (Arabidopsis thaliana), 5'ss of exon 4
TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaactaccatcctttttccatgcttctgctgctgatttcctttgttcgtcaatatatgataataacctgtgagtgttttttttacttctgttgcggtgcatattcag
||||| ||||| ||||| ||||| || || ||||| |||||  ||||||||||||||||||| |||          |  | ||  ||       | | ||||| | ||| | |  ||  ||||   || |||  |||   |||| ||  |  || | | |              
TCTCTGATGATTGCTGCAATTCCCAATATTATTGGATGGCTTTCGATATCATTTGCAAAAgtgagt------gttttggtgttctcaaa-----gtttctgatattcttggcttatctctatacc-tactaagttgttgttgttcttggtttttgtttag--------------

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|50325333|gb|CO520459.1|CO520459
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCT
EST: gi|148987704|gb|EE031592.2|EE031592
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTGGGT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
EST: gi|71766862|gb|DR964799.1|DR964799
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAAGATTTGGAGTTGGT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
EST: gi|50325566|gb|CO520692.1|CO520692
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCT
EST: gi|21390663|gb|BQ528712.1|BQ528712
EST:     TATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
genomic: TATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
EST: gi|148964510|gb|EC905855.2|EC905855
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
EST: gi|71331313|gb|DR802490.1|DR802490
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAAGATTTGGAGTTGGT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
EST: gi|148991896|gb|EE033498.2|EE033498
EST:     TCGCTGCGATTCCAAAAATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCCTCTTTCTTGTTTATGG
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCC-TCTTTCTTGTTTATGG
EST: gi|148958173|gb|EC904377.2|EC904377
EST:     TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA                         GATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT
genomic: TCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGT

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: 107

TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGTGTAATATCGTATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGTGTAATATCGTATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGTGTAATATCGTATACA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 162

TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAAgtaagttcaa ... gcatattcagGATTCCTCTTTCTTGTTTATGGGTCGGCTGCTAGAAGGATTTGGAGTTGGTGTAATATCGTATACA