Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag

Basic information

species Zea mays
transcript GRMZM2G063355_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 1
CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcg----ttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag
|| ||||||| || ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||||| | |||||| || ||| ||| | || | || |||||| |||| | | | || | ||| ||| ||| ||||||| ||||
CGCGCACCGTGTCGGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgtaggcctcttctccgttgctccccctcctctgtagggtttggtacccgattgctgtgggtttgggtggggcgtctgatcgatctcggtgg-gtgtttcctgtgcag----

upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 1
CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag
|| ||||||| || || |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||||| | |||| ||| |||| | |||| |||| | | | ||| ||| ||| | |||| ||| | || || |||| ||| | |
CGCGCACCGTGTCGGCCTTCCTCGACAAGGGCGTCCTCTCCGTCCCCGAGTTCATCCTCGCCGGCGACAACCTCGTCTCCAAGTGCCCCACCTGGTCCTGgta-gctctctcctcccctccgtt-gctccccctcaat-tgctgggtttgggt--ttgg-gtttgggtggc-gtctcatcgatccccc-tgtgtag-----------

upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G36540.1 (Glycine max), 5'ss of exon 1
CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggtt--gctgattgg-----ttggttgactgattgatctggtgtgt---ttcgtgtgttcacag
| | ||||| ||||| ||| || || || || ||| ||| |||||||| | ||||||||| || ||||| ||||| ||||||||||||||||||| |||| ||| | | | || | ||| | || | | || | || || | | |||| ||||| | ||||| | || | | ||
CCCGAACCGTTTCCGCCTTCAAAGAAAAAGGAGTTCTCAGTGTCTCCGAGTTCGTCACCGCCGGCGATAATCTCGTTGCCAAATGCCCCACCTGGTCCTGgta-attctaattttcatttttccgtcttttcctgattatattcaaattgcctcttttagcctttcgaaatcccaatttgaatgatttagtaaatgtgtgattctgttttccaatag

upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ14759 (Selaginella moellendorffii), 5'ss of exon 1
CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctctcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag
| |||| ||||| || ||| ||||||| ||||| || | | | || ||| | | ||||| ||||| ||||||||||||||||| ||||||||||||| | | || | || | | ||| | || | | | || |
CTCGCACGGTCTCGGCATTCGTCGAGAAAGGCGTGCTGACTCCCGCGGAATTCGTCCAGGCCGGTGACAATCTCGTCGCCAAGTGCCCTACCTGGTCCTGgtatgatacgctacctaaagtcccttgtttacctattttcttcc--tcctctttctcgcag----------------------------------------------

upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ26505 (Selaginella moellendorffii), 5'ss of exon 1
CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctcctttcctc-tcccctcgctctgcctccctctaaccgatttaggtggttgctgattggttggttgactgattgatctggtgtgtttcgtgtgttcacag
| |||| ||||| || ||| ||||||| ||||| || | | | || ||| | | ||||| ||||| ||||||||||||||||| ||||||||||||| | | || | | |||| | | | ||| | | | | | |
CTCGCACGGTCTCGGCATTCGTCGAGAAAGGCGTGCTGACTCCCGCGGAATTCGTCCAGGCCGGTGACAATCTCGTCGCCAAGTGCCCTACCTGGTCCTGgtatgatacgctacctaaattcccttgtttacctattttcttcctcctctttctcgcag-------------------------------------------------

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|211036315|gb|FL466133.1|FL466133
EST:     CTCGCCGGCGACAACCTCGTCGCCTAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGAGCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: CTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|33770858|gb|CF273152.1|CF273152
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211327140|gb|FL012759.1|FL012759
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211327148|gb|FL012767.1|FL012767
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211324977|gb|FL012746.1|FL012746
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211329311|gb|FL012773.1|FL012773
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211327149|gb|FL012768.1|FL012768
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211327147|gb|FL012766.1|FL012766
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|148971664|gb|EE022387.2|EE022387
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|26559206|gb|CA831441.1|CA831441
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|15208976|gb|BI430860.1|BI430860
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGAATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211329317|gb|FL012779.1|FL012779
EST:     TCATTCTCGCCGGCGACAACCGTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TCATTCTCGCCGGCGACAACC-TCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211324974|gb|FL012743.1|FL012743
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211324988|gb|FL012757.1|FL012757
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|50331765|gb|CO526891.1|CO526891
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211327141|gb|FL012760.1|FL012760
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|22542051|gb|BU092489.1|BU092489
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
EST: gi|211327145|gb|FL012764.1|FL012764
EST:     TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTG                         GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA
genomic: TTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 51

CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

CGTGCACCGTCTCCGCGTTCCTCGAGAAGGGCGTCCTCTCCGTCCCCGAGTTCATTCTCGCCGGCGACAACCTCGTCGCCAAGTGCCCCACCTGGTCCTGgtgcgttctc ... gtgttcacagGGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG