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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcctgtgaatcaactacctccattttgatttattttaaaaccattcttttcctttccttttttttgtgttactttagccatttgtatcttgttcaaaatcttgtccacaatttgttacatctatcttcatgttggcag

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 4
CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcctgtgaatcaactacctccattttgatttattttaaaaccattcttttcctttccttttttttgtgttactttagccatttgtatcttg-ttcaaaatcttgtccacaatttgttacatctatcttcatgttggcag
 |||||||| || || |||||||||||||||||||| ||||||||||| |||||||||||||||||||| || ||||| || || |||||||| ||||| ||||    |     ||| ||| | |||  | | || ||||  || |   | | ||||  ||| ||  ||| |  || ||| |     ||||  | || ||||  || || ||| || | ||                        
TGGTCATGGTTCCAATGTTCAGGGCCTTGAAACAACCGCCACATTTGACCCAAAGACTGATGAGTTTGTTATACACAGCCCGACACTGACCTCTAGCAAGgtaatactcct---atctact-cttcctctcttatctatt--aagatgctacatttc--ttctttaatttggaatttcttcaatatcttgttgcatggttcatgattttatcccca-tgtgcag---------------------

upper sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 3
CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcctgtgaatcaactacctccattttgatttattttaaaaccattcttttcctttccttttttttgtgttactttagccatttgtatcttgttcaaaatcttgtccacaatttgttacatctatcttcatgttggcag
 ||||||||||| || ||||| |||||||| ||||| || || |||||||||||||| ||| ||||| |||| ||||||||||||| ||| ||   |||||||| |      |||  |   ||    || |   || || |   |    ||   ||   |  |||  |||||| ||  || |  |||| |                                                      
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaagggg--aagaagtatagacagttatctattttgatctctgagtgtttaaattg--tgtcttgattttgttttgtttgaaacattag------------------------------------------------------

upper sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 5'ss of exon 4
CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcctgtgaatcaactacctccattttgatttattttaaaaccattcttttcctttccttttttttgtgt-tactttagccatttgtatcttgttcaaaatcttgtccacaatttgttacatctatcttcatgttggcag
 |||||||||||||| ||||| || ||||| |||||||||||||||||||| ||||||||||||||||| || |||| |||||||| |||  |   ||||||||      ||  | |||  | |      |||| | ||| |  |    |||| ||  ||   |    |||   | |   ||     |||| ||                                                   
TGGTCATGGCTCAAATGTTCAAGGACTTGAGACAACTGCCACATTTGATCCCAAGACTGATGAGTTTGTAATTCACACTCCAACTCAGACTGCATCCAAAgtaa------gtataccaagaagcctttgattgagt-attatgcacagtttctcttggttgtgtaagattttcatctgtcttgattgtttgaatag-------------------------------------------------

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|78109870|gb|DV528286.1|DV528286
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|78092061|gb|DV520435.1|DV520435
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|18963249|gb|BM660327.1|BM660327
EST:     CAAAGACTGATGAGTTTGTCATCCACAGCCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|78118216|gb|DV536603.1|DV536603
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|71438097|gb|DR819147.1|DR819147
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|149044450|gb|EE047571.2|EE047571
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|148952746|gb|EC898728.2|EC898728
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|149089538|gb|EE178785.2|EE178785
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|32934681|gb|CF039493.1|CF039493
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|213184355|gb|FM193741.1|FM193741
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TNNNGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|149096635|gb|EE182400.2|EE182400
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|78089952|gb|DV518326.1|DV518326
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|71315288|gb|DR794256.1|DR794256
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGGAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
EST: gi|149106570|gb|EE188463.2|EE188463
EST:     CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAA                         TGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT
genomic: CAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCT

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), 49 (downstream exon)
Score: 177

CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 459

CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 464

CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 686

CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcct ... atgttggcagTGGTGGCCTGGTGGCTTGGGGAAAGCTTCCACTCATGCAGTGGTGTATGCTCGGCTGATAACTGAAGGAAAGGACTATGGTATACATG