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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccagcctgctacattacactcagtatcttgtttcttcgcaggcacttgggaagttttgtgcccagatgaaccacattgataactagttgatgga...

Basic information

species Zea mays
transcript GRMZM2G022876_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022876_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g34950.2 (Oryza sativa), 5'ss of exon 2
-----TGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccagcctgctacattacactcagtatcttgtttcttcgcaggcacttgggaagttttgtgcccagatgaaccacattgataactagttgatgga
     |||| | |  ||||| |  |||||||| |||||||| ||||||||||| || ||||| || |||||||| ||||||||||||||||||||  |||| ||||||  | ||  |  | | |||  |      || | |||| |  | |     |    || ||| ||| |||  | ||  ||| ||| |   || | |||  
GTTGTTGGTATAGTTAATGCAAAGACTGGGGTCAACAAACCCGAATTGCTTCCCAAGGAATTCACCACCGTCATTGATGTTGCTGGTTTTCTCTCCCCAGgtcaggtaaattcaaacaac-atattctat--gagatgtagtttttcagaactagttacaaaaatttagtgtcca--ttaaaaacactgagatgcagatcatgac

upper sequence: GRMZM2G022876_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g34950.1 (Oryza sativa), 5'ss of exon 2
----TGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccagcctgctacattacactcagtatcttgtttcttcgcaggcacttgggaagttttgtgcccagatgaaccacattgataactagttgatgga
    |||| | |  ||||| |  |||||||| |||||||| ||||||||||| || ||||| || |||||||| ||||||||||||||||||||  |||| ||||||  | ||  |  | | |||  |      || | |||| |  | |     |    || ||| ||| |||  | ||  ||| ||| |   || | |||  
TTGTTGGTATAGTTAATGCAAAGACTGGGGTCAACAAACCCGAATTGCTTCCCAAGGAATTCACCACCGTCATTGATGTTGCTGGTTTTCTCTCCCCAGgtcaggtaaattcaaacaac-atattctat--gagatgtagtttttcagaactagttacaaaaatttagtgtcca--ttaaaaacactgagatgcagatcatgac

upper sequence: GRMZM2G022876_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G52970.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccagcctgctacattacactcagtatcttgtttcttcgcaggcacttgggaagttttgtgcccagatgaaccacattgataacta-gttgatgga------------------------------------------------------------------------------
 || || ||  |||| | |  ||| || |||||||||||||||||||||||||| || ||| | || || |||||||||| ||| |||||    || ||||||  | ||  ||  |||  | ||   | | |   | ||      | |||||||     | ||     ||  || | |   ||| | | |  || |||                                                                                 
GGGGTTTGCAGATGCAAAAGTTGGTGTTAACAAACCAGAATTGCTTCCTAAAGAGTTCACTTCTGTTATAGATGTTGCTGATTTCCTCTCTAATGGTCAGgta--tgcatgcttgtaccatccatctatttttgaggtttgattaaagcacttgtttcttgttaatgtcatgtggatctatttgcttattctgtagatttttagtgtatttctgattttgaatgttttcgccgcttttggttttcttttcttaatgatgttgttctttgagagttatag

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|211533933|gb|FL079631.1|FL079631
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACA
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACA
EST: gi|211533938|gb|FL079636.1|FL079636
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211533932|gb|FL079630.1|FL079630
EST:     AGAATTTACTACCGTCCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTG
genomic: AGAATTTACTACCGTC-ATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTG
EST: gi|211536947|gb|FL079648.1|FL079648
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGNCAG                         GAAAACCGTTTGCGCCAAGAGATAGA-GACCTG
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTG
EST: gi|211539949|gb|FL079654.1|FL079654
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGAC-TGGAG
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAG
EST: gi|13125853|gb|BG316423.1|BG316423
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211539950|gb|FL079655.1|FL079655
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211533934|gb|FL079632.1|FL079632
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGA
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGA
EST: gi|211536951|gb|FL079652.1|FL079652
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAG
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAG
EST: gi|211246142|gb|FL441753.1|FL441753
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211536937|gb|FL079638.1|FL079638
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCACGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211536944|gb|FL079645.1|FL079645
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211539948|gb|FL079653.1|FL079653
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211536943|gb|FL079644.1|FL079644
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCC

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: 49 (upstream exon), 21 (downstream exon)
Score: 6

TGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG




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