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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtagatgctgattacctgattttcagagttttaggaatgtttcatggtat...

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtag-atgctgattacctgattttcagagttttaggaatgtttcatggtat---------
 ||||||||| ||||||||||||||||||||||||| ||||| ||||||||| ||||||||||||||||||| || ||||| ||||  |||||||||||||| |  |||| |  |||          |||  | || || |||||| | |||||    ||  ||| | | ||||    |   ||           |||  |         
CAAAGGTTGTAGTGATGTTTATGCATCATTTGATAAATATGTCGAAGTGGAGCGTCTAGAGGGTGATAACAAATATCATGCAGAGCAGTATGGCTTACAGgtactgacaaatcctgc----------actccgaagttgaatattttgatgtagtgaacttcttagcaggtttttttgggagtacatgatacatgtggagtaaatttagg

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 4
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtagatgctgattacctgattttcagagttttaggaatgtttcatggtat-----------------------------------------------------------------------------
 ||||| |||   || || ||||| || |||||||||||||||||||||||    || ||||||||||||||||| ||||| ||||  ||||| ||||||||     |      ||   | |   |   ||  |  | || ||       |||  |||   |||  |  | || |  |||| |  |   ||| |    |                                                                              
CAAAGGCTGTAAGGACGTATATGCTTCTTTTGATAAGTATGTGGAAGTGGAACAACTTGAGGGTGATAACAAGTATCATGCTGAGCACTATGGTTTACAGgtaaaacctgaacatgtgtttttgcttttttgttgtcaggctaaccttcagtatgtgc--gttattttttgttaattgtttgattatctttttacatcacttttgttggttgttgttgttaaattcgtattttagaatgattattttcctagaacgtgattatgattaccctttcag

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttc-ccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtagatgctgattacctgattttcagagttttaggaatgtttcatggtat-
||| || |||| |||||||||||| || ||||| |||||||| ||||| ||  |||| || || |||||||| || |||||||| |  ||||| || ||||||  |  ||| | ||  | |  |  |    |||||    |  ||||  ||  |  | |||| |   | | ||     |||    | |       || | | 
GAAGGGCTGTCCTGATGTTTATGCTTCCTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgtttgctgcaattgtttattttggaatctacttgtaataagtcattt--gtagaagttctgaatcttttagttcttatgttgggtgtacaaaaattgttttg

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G16170.1 (Glycine max), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaagttttgctctatgcgtgactttgtagctggatat-ttaggtgtagatgctgattacc-tgattttcagag-----ttttaggaatgtttcatggtat
 ||||||||||||||||||||||| || |||||||||||||| ||||| || ||||| ||||| |||||||| || ||||| || |  ||||| || ||||||      ||||    |   |   ||     | ||||    || |||  |||||| | | |      || |||||| ||     || |   ||  | |  || || 
TAAAGGTTGTCGTGATGTTTATGCTTCCTTTGATAAGTATGTCGAAGTTGAAAGTCTTGAGGGGGATAACAAATATCATGCTGAACAGTATGGTTTGCAGgtt------agttgctattcttaaatgctgaagcagcttataatattatttgtagaagttaaccttagtgtttttcaaagaatttttctgtaaacttattttgata-

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttc-ccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtagatgctga-ttacctgattttcagagt---tttaggaatgtttcatggtat
|||||| |||| |||||||||||| || ||||| |||||||| ||||| ||  |||| || || |||||||| || |||||||| |  ||||| || ||||||     ||| | ||  | |  |  |    |||||    |  ||||  ||  |  | |||| |    |  || | | | |   | ||  ||  |    | |   
GAAAGGCTGTCCTGATGTTTATGCTTCCTTTGACAAGTATGTTGAAGTTGAACGTCTTGAAGGGGATAACAAATATCATGCGGAACAATATGGTTTGCAGgttggttgcaattgtttattttggaatctacttgtaataagtaattt--gtaaaagttctgaatcttttagttcttatattgggtgtacaaaaatcattttg---

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttc----ccacaagttttgctctatgcgtgacttt-----gtagctggatatttaggtgtagatgctgattacctgattttcagagttttaggaatgtttcatggtat
 |||||||||| |||||||||||| || ||||||||||| || ||||| ||| | ||||| || |||||||| || ||||| ||||   |||| || ||||||     | ||| || ||   | | || | | |||     | || |   |   ||  |||| || || |  |  |   ||||| | |||||    || ||        
CAAAGGTTGTCATGATGTTTATGCTTCTTTTGATAAGTACGTAGAAGTTGAGCGCCTAGAAGGGGATAACAAATATCATGCTGAGCACCATGGATTGCAGgttagttgctacatgtatttaacaaagcctaatttttaggtgcaggttagttgctatatgtatat-ctaacaaagttgatttcatacttttataggtgctt--------

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtagatgctgattacctgattttca-gagttttaggaatgtttcatggtat
 ||||| ||||| ||||||||||| |||||||| |||||||| || || ||  |||| ||||||||||| ||||| ||||| ||     ||||  ||||||||     |         |  ||| |   |   |   |  |  |||   | ||  | ||||  | || |     | ||    ||  |  |||| ||   ||
CAAAGGCTGTCGCGATGTTTATGCTTCATTTGACAAGTATGTTGAGGTTGAACGTCTCGAGGGTGATAATAAGTATCATGCTGAAATCCATGGGCTACAGgttagttgacaccaaaaacattgcatctttaaattttttcaactttgtat-tatttcctgaggaacttaaaccaatgaagcatacaatggttttatcagat

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 8
lower sequence: EFJ19227 (Selaginella moellendorffii), 5'ss of exon 8
GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaagttttgctctatgcgtgactttgtagctggatatttaggtgtagatgctgattacctgattttcagagttttaggaatgtttcatggtat
 || || ||    || || ||||| |||||||| ||||||||||| || ||||  || ||||| ||||| ||||||||||| || |   |||| || |||||  ||      ||  |  |  |  ||    ||     || | |  |  || ||                                              
CAAGGGCTGCAAGGACGTGTATGCGTCATTTGACAAGTATGTGGAGGTTGAGAAACTTGAGGGGGATAATAAGTACCATGCCGAACAGAATGGTTTGCAGgtgaccttcctattcacgtttagaatgcagctg--atgggctttcaaattgcag----------------------------------------------

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|5439328|gb|AI820249.1|AI820249
EST:     AGGGTGAT-ACAAGTACCATGCGGAGCGTTATGGCTTACAG                         GATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
genomic: AGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
EST: gi|5740126|gb|AI947816.1|AI947816
EST:     TACCATGCGGAGCGTTATGGCTTACAG                         GATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
genomic: TACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
EST: gi|101389686|gb|EB816777.1|EB816777
EST:     AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAG                         GATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
genomic: AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
EST: gi|76920464|gb|DV168186.1|DV168186
EST:     AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAG                         GATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
genomic: AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
EST: gi|78026582|gb|DV494969.1|DV494969
EST:     AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAG                         GATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
genomic: AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
EST: gi|5398807|gb|AI812151.1|AI812151
EST:     AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAG                         GATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT
genomic: AGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTT

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: 47 (upstream exon), 47 (downstream exon)
Score: 200

GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATACAATGGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATACAATGGTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 199

GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATACAATGGTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 155

GAAAGGTTGTCGTGATGTTTATGCATCATTTGATAAGTATGTGGAAGTGGAGAGTCTAGAGGGTGATAACAAGTACCATGCGGAGCGTTATGGCTTACAGgttcccacaa ... ttgttttcagGATGCAAGGAAAGGTGTGCTTTTCCTTGATTTCCCTCCTGTTTTGCAGCTTCAACTGAAGCGTTTTGAATATGATTACATGCGAGATACAATGGTTAAG