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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatcacaaaattattgaatcaatttcactaataaactactgcccttttgaacccctccttgtctgtatttaattgtcaattagaccttgtatata...

Basic information

species Zea mays
transcript GRMZM2G105494_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105494_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g17680.1 (Oryza sativa), 5'ss of exon 4
GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatcacaaaattattgaatcaatttcactaataaactactgcccttttgaacccctccttgtctgtatttaattgtcaattagacc--ttgtatata------
|||||||||||||||||||| ||| |||||||||| || ||||||||||||||||| ||||| |||||| ||||    | || | |  ||  || | | || |   ||   ||  ||      |     | |   |    |||||||||  ||| |   | | |||||      
GTGAGGAAGGAGAAGCTAGGTGATAGAATAACTGCCCTTCACCAGCTTGTCTCCCCATTTGGGAAGgtacatat----atatcactacatgcatgttattagt---ctttagcttttagatttcaacaatgggaagagaataattgtca-ctaggctagtagaatataacaact

upper sequence: GRMZM2G105494_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G21770.2 (Glycine max), 5'ss of exon 4
GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatcacaaaattattgaatcaatttcactaataaactactgcccttttgaacccctccttgtctgtatttaattgtcaattagaccttgtatata-------
||||| |||||||||||||| ||| ||||||| ||||| |||||||| || ||||| || ||||||||| |||  ||||||  ||| ||| | |   |    || |    | | |  |  |  | | |    |    |    |    | | || ||| |   || |       
GTGAGAAAGGAGAAGCTAGGTGATAGAATAACAGCTCTTCACCAGCTAGTTTCCCCATTCGGAAAGgta-ataa-acaaaaccatt-aattattacaatcgctaca----tacacaataaacactcacaaaatacaaaaactagaaaccaataaaccataattacaaagcgcc

upper sequence: GRMZM2G105494_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G02020.2 (Glycine max), 5'ss of exon 1
--GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatcacaaaattattgaatcaatttcactaataaactactgcccttttgaacccctccttgtctgtatttaattgtcaattagaccttgtatata-----
  ||| |||||||||||||||| ||| |||||||  | || ||||| || || ||||||||||||||||||   | |   |  |||    |||| ||    |||||||| |    || |    | || |    |     |    |||   | |  | | |||| | |      
AGGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAGgtaatcaactatactttaactgatcagttattataataaacaaa---ccatacacaaccataagagaagagaaaccattacaagt--gcctttgtgtttggtttt

upper sequence: GRMZM2G105494_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G02020.1 (Glycine max), 5'ss of exon 4
GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatcacaaaattattgaatcaatttcactaataaactactgcccttttgaacccctccttgtctgtatttaattgtcaattagaccttgtatata-----
||| |||||||||||||||| ||| |||||||  | || ||||| || || ||||||||||||||||||   | |   |  |||    |||| ||    |||||||| |    || |    | || |    |     |    |||   | |  | | |||| | |      
GTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAGgtaatcaactatactttaactgatcagttattataataaacaaa---ccatacacaaccataagagaagagaaaccattacaagt--gcctttgtgtttggtttt

upper sequence: GRMZM2G105494_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g04120.t01 (Vitis vinifera), 5'ss of exon 4
GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatcacaaaattattgaatcaatttcactaataaactactgcccttttgaacccctccttgtctgtatttaattgtcaattagaccttgtatata---
||||| ||||||||||| || ||| ||||||| || || |||||| | || ||||| ||||||||||||   ||| |||  |  ||   ||   | | ||       |||||  |           ||         | ||  || | ||  |  || |  | | |   
GTGAGAAAGGAGAAGCTGGGTGATAGAATAACAGCCCTTCACCAGTTAGTTTCCCCATTTGGAAAGgta---atcccaagctggttctctctcctcctcttgactcatactgaacaggaaggaatatcacacaagccaattttttatgaacaaacccataaagagattt

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|78084337|gb|DV512730.1|DV512730
EST:     TAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG                         ACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTC
genomic: TAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTC
EST: gi|76929547|gb|DV172057.1|DV172057
EST:     TAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG                         ACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTC
genomic: TAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTC
EST: gi|71435603|gb|DR816653.1|DR816653
EST:     TAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG                         ACTGACACAGCGGCTGTACTCCTTGAAGCCATTGGGAACATCAGATTCCTC
genomic: TAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTC

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), 45 (downstream exon)
Score: 41

GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG


Block sizes: 42 (upstream exon), 29 (downstream exon)
Score: 8

GTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAGgtatatatca ... ttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG