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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcactagcatatttgcctgatcatgattttcgtctctactgtggctaaattgcaatcattcacaacttttatctagtatagcgtaatggttaag...

Basic information

species Zea mays
transcript GRMZM2G150772_T02
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150772_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 5'ss of exon 21
TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttca----------ctagcatatttgcctgatcatgattttcgtctctactg-tggctaaattgcaatcattc-------acaacttttatctagta-tagcgtaatggttaag---
| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| |||||||||| |||          |||   | ||| |   | || |||       | | ||| || || || |||||  |||        |  | ||| ||  | || |  |   ||| || |    
TCTTGAAAGATGAGTTCCTGCGTTCCAGAGATTATCCTCAATGCCCTCCAACTTCTCATCTGTTCCAGCGTTTCCGGGAGTTGGGATATGCATGCATAAAgtatggtcaactatgctctctatttttttttctgaaacaggataccatcttgtcctgatgtctcaactgcaaatatttgtttgaaatgattttgattaaataatttctctatgctttacaag

upper sequence: GRMZM2G150772_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA17G20310.1 (Glycine max), 5'ss of exon 22
TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcactagcatatttgcctgatcatgattttcgtctcta-ctgtggctaaattgcaatcattcacaacttttatctagtatagcgtaatggttaag---
||||||||||||| || ||||| ||||||||||||||  |||| ||||| || |||||| | || || || ||| |  | ||||| ||||| ||||| | ||| |   | ||  | |||||    ||  || ||||  | |  |  | ||    |    | ||  ||   || ||   |  | |||| | |  | |   |    
TTTTGAAAGATGAATTTCTGCGTTCCAGAGATTATCCAAAATGTCCTCCAACATCTCATTTATTTCATCGATTCAGGCAGTTGGGTTATGCCTGTATCAGgtaggcaaaataagaaatttg----attgtgcttttgatattgaattatgatgcatgctccattttttctaatttgcttaaactatatctttctcgaggatttt

upper sequence: GRMZM2G150772_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA05G10590.1 (Glycine max), 5'ss of exon 22
TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcactagcatatttgcctg-atcatgattttcgtctctactgtggctaaattgcaatcattcacaacttttatctagtatagcgtaa---tggttaag
||||||||||||| || ||||| ||||||||||||||  |||| ||||| || |||||| | || || || ||| |  | ||||| ||||| ||||| | ||| |   | ||| | |||||  ||     |   | | |||  |  |     || | | || | |   ||||    |||  | | ||  || |   || ||   
TTTTGAAAGATGAATTTCTGCGTTCCAGAGATTATCCAAAATGTCCTCCGACATCTCATTTATTTCATCGATTCAGGCAGTTGGGTTATGCCTGTATCAGgtaggcaaaataggaaatttgattgtgcttttgatattgtcattg-tacatatagaattcattgaactacaatgcatattcaatttattgttaatttgctt---

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|149014442|gb|EE044051.2|EE044051
EST:     ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAA                         GTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
genomic: ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
EST: gi|32839168|gb|CD978849.1|CD978849
EST:     ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAA                         GTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
genomic: ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
EST: gi|32837707|gb|CD977385.1|CD977385
EST:     ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAA                         GTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
genomic: ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
EST: gi|32838041|gb|CD977719.1|CD977719
EST:     ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAA                         GTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA
genomic: ACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 148

TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCACGAGAGCATGCTGGATCTATTTATTTGTCACCTGAACCCAAGTGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCACGAGAGCATGCTGGATCTATTTATTTGTCACCTGAACCCAAGTGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCACGAGAGCATGCTGGATCTATTTATTTGTCACCTGAACCCAAGTGCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCCCTCCCACTTCTCATCTGTTCCAGCGTTTCCGAGAATTGGGATATGCATGTATAAAgtatgttcac ... atatttccagGTATGGTCAGTTTGACAGTGCAAAAGAAACTTTTGAGGTTATTACAGATCACGAGAGCATGCTGGATCTATTTATTTGTCACCTGAACCCAAGTGCATTG