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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgccgacatataagatgcacataattctgaattatagccttttggtttggacgtggctacggacatattggattttctgcttgtgacag

Basic information

species Zea mays
transcript GRMZM2G030138_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030138_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 5'ss of exon 5
CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgccgacatataagatgcacat-aattctgaattatagccttttggtttggacgtggctacggacatattggattttctgcttgtg--acag
| ||| ||||| | ||| |   ||||||||| || ||||| || ||||||||||| || |||||||||||  | |||||||||||||||||||||||||||||||||||  | | || | ||||| || || | ||||||  |   ||      || |       | |||| | || | | || || || ||   |||
CTCCCATTGAGTTAGATGTGAATGGCTCCAAAGTTTCTGTCCTTTACCTGGACACTGAGGGATTTGAGAGCATCGGAAAATCAAATGTATATGATGATAGgtttgttgcttatagatgaaatgcatattaagtttgaattggaattttaaatggtgaaaa-----atggac-tgttagttcttttgtttttgttgcag

upper sequence: GRMZM2G030138_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G03660.1 (Glycine max), 5'ss of exon 5
CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgccgacatataagatgcacataattctgaattatagccttttggtttggacgtggctacggacatattggattttctgcttgtgacag
| ||  | ||  |||||||   |||    |     |||||  | ||||| || || ||||||||||| |||||||| || || ||||||||||||||| |||   ||||   || || |      |    |||||  ||  | | | |  | |||    | | |       | |||  ||| ||  |||      
CACCTATAGATTTGGATATTAATGGAGTAAGAACTTCTGTCTTTTACCTTGATACAGAAGGATTTGAAAGTGTTGGGAAGTCCAATGTATATGATGATCGgta-attgctttcagatcatgcattctgtgttctgtgttgaatcatatatgattg--tttagttggctttttcttgtgtttgct-tttgcag---

upper sequence: GRMZM2G030138_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G16130.1 (Glycine max), 5'ss of exon 4
CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgccgacatataagatgcacataattctgaattatagccttttggtttggacgtggctacggacatattggattttctgcttgtgacag
| ||  | ||  |||||||   |||    |     |||||  | ||||| || || ||||||||||| |||||||| || || ||||||||||||||| |||   ||||   || || |      |    |||||  ||  | | | |  | |||    | | ||      | |||  ||| ||  |||      
CACCTATAGATTTGGATATTAATGGAGTAAGAACTTCTGTCTTTTACCTTGATACAGAAGGATTTGAAAGTGTTGGGAAGTCCAATGTATATGATGATCGgta-attgctttcagatcatgcattctgtgttctgtgttgaatcatatatgattg--tttagttagctttttgttgtgtttgct-tttgcag---

upper sequence: GRMZM2G030138_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 5
CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgccgacatataagatgcacataattctgaattatagccttttggtttggacgtggctacggacatattggattttctgcttgtga-cag
| ||  | ||| |||| || | |||    ||    || ||  | ||||| ||||| || ||||| || ||||||||||| |||||||| ||||||||  |||      || | |    || |||| | | ||    |||  | | |||   |  ||| |     |    |  ||    || | ||    |   |||
CACCATTAGAGCTGGAGATTGATGGAGTAAAAACTTCCGTAATTTACCTCGACACTGAGGGATTCGAAAGTGTTGGAAAGTCAAATGTTTATGATGACCGgt-----acccagac---agttgca-acatttgcacatttaaacttttctttgcggaagctctgaatatctaatcaatttctgtgtaaatattcag

upper sequence: GRMZM2G030138_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S100_89V6.1 (Physcomitrella patens), 5'ss of exon 5
CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgt-------tgccgacatataagatgcacataattc--tgaattatagccttttggtttggacgtggctacggacatattggattttctgcttgtgacag------------------------------------------------------------------
  ||  | ||  |  |  |||  ||    |||   || ||  ||| | ||||||| ||||| ||||||||| ||||||| || ||||| |||||||||||||   |       ||  ||  | || |   |||||  | |  |     | | | |  | ||         || |    ||||     ||   |  || ||                                                                      
AGCCTCTGGAAATCAACCTCGACGGTGTGAAGACCTCGGTCTTATTCTTGGACACGGAAGGCTTTGAGAGTATTGGAAAGTCCAATGTTTATGATGATAGgtacatatctccgtggtgaactttatgcaacacattgtaccttttgcgaaaacgtaatagtcgaagtaccgcaatacgcatacgcctttacttaattatgctgtgtcgcattagtaagagctggttgtgaagttctgtttcatgactcgagtgtgaactttggtatgcag

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|76924745|gb|DV170113.1|DV170113
EST:     GACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAG                         GATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCC
genomic: GACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgcc ... cttgtgacagGATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCC
EST: gi|89763546|gb|DY690690.1|DY690690
EST:     GACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAG                         GATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCC
genomic: GACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgcc ... cttgtgacagGATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCC
EST: gi|71449828|gb|DR830878.1|DR830878
EST:     GACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAG                         GATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCC
genomic: GACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgcc ... cttgtgacagGATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCC

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 1 RNA-Seqlibrary.


Block sizes: 46 (upstream exon), 27 (downstream exon)
Score: 11

CCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATCAAATGTATATGATGATAGgtttgttgcc ... cttgtgacagGATATTTGCTCTGGCAACTGTTTTAAGTTCTGTTCTGATCTACAATCTTCCTGAAACA




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