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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaacagttaattgtgcatgcatctaggtccccaggttctaagagattataaccgtcattgattgaattatgactcttaagacactgatactctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT

Basic information

species Zea mays
transcript GRMZM2G340359_T02
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340359_T02 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 14
agtaacagttaattgtgcatgcatctaggtccccaggttctaagagattataaccgtcattgattgaattatgactcttaagacactgatac-tctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT
  | | ||  ||         |   |  ||       | ||   |   || ||   ||     ||     |    |   |  |||  | |   | |||||| || ||    |  |  |||| || |||||||||||||| ||||| |||||  |||| | |||||||||||| |||||||| ||||| |||   ||| |||
gtttatagaaaagcaaaggcaccgatgagtaattgtctacttgcaatgtaaaaaaatc-ccatttcgtccactgatggcacaacaacgttctgtgtgacagCAGGGCCCCGCAGGTGCATCGCATTGGAGAAGCATCAAGCAGCACGTGCTACCTCATGGTTCTTCAAGGCCCTTCTCCCGGAAGCACTCCATGGACGCCT

upper sequence: GRMZM2G340359_T02 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g46450.1 (Oryza sativa), 3'ss of exon 20
-agtaacagttaattgtgcatgcatctaggtccccaggttctaagagattataaccgtcattgattgaattatgactcttaagacactgatactctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT---
 |   | |   ||  |  |       ||  |  | |  ||  ||   |  | || |    ||  |  | | ||| | |  |  ||  |     | |||||| || ||    |  |  |||| || |||||||||||||| ||||| |||||  |||| | |||||||||||| |||||||| ||||| |||   ||| |||   
tatagaaaagcaaaggcaccgatgagtaattgtctac-ttgcaatgtaaaaaaatcccatttcgtccactgatggcaca-acaacgtt--ctgtgtgacagcagGGCCCCGCAGGTGCATCGCATTGGAGAAGCATCAAGCAGCACGTGCTACCTCATGGTTCTTCAAGGCCCTTCTCCCGGAAGCACTCCATGGACGCCTCGT
















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|60358558|gb|DN225531.1|DN225531
EST:     GATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTC
genomic: GATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... actctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTC
EST: gi|93012875|gb|EB638395.1|EB638395
EST:     GATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAG                         GAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTC
genomic: GATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... actctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTC

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), 46 (downstream exon)
Score: 49

GAACACTGTCCAAACTGGATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... actctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 23

GAACACTGTCCAAACTGGATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... actctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 14

GAACACTGTCCAAACTGGATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... actctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

GAACACTGTCCAAACTGGATTTGATAGGACCGTTGCTTTTTGTAATCAAGAGAAGCAAAGAAATGAGgttagctgtt ... actctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattataaccgtcattgattgaattatgactcttaagacactgatactctgacagGAGAGCTTGCCGTGCACATCCCACTGGAGAAGCATCAAACAGCATGTGCTCTCTCAGGATTCTTCAAGGCCTTTCTCCCGAAAGCATTCCTCAGACACCT
             attgattgaattat  TA-rich tract