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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC

Basic information

species Zea mays
transcript GRMZM2G179308_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
||||| ||||||||| ||  ||  | ||||    |   |||     | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||||||||||||| || |||||||| || ||||||| ||||| | |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| || |
gtatactttgttcttctacctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 6
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttag---tgaatattgaata--tggtactgatcctc--tttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
                                   | | | |     ||  |||  ||   ||| || |  || ||||| ||      | ||   ||   ||  |   ||      || |||  ||||   ||  | || || |||| ||||      | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |       
--------------------------------aggaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgagatcactgacatccattgctgattgtttatatttaacagAGTACAACCAGATCACCAA------GTTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagt----gaatattgaata-tggtactgat--cctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
                                  || | | |     ||  |||  ||   ||| || |  || ||||| ||     |||   |||  | ||  |   ||  | | || |||  ||||   ||  | || || |||| ||||      | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |       
--------------------------------ggaaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgct-tgttgatttctgttgtaataggttagtgaa-tattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
                                      | || || |       || |||       |  |||       || | || |  ||||   || | |  |  |  | ||| |   |||  ||     |||||||  | || ||| | || ||||   ||  | ||||| || || ||||| || ||||||||||||||||||||||| || ||||| |  |      
-------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaa---ggaatt--tggttgtgtttcctgatgcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtatatttt--gttctttt--atttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttag---tgaatattgaatatggtactgatcct----ctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                    |||  ||||   ||  |||  | ||   |        |||     |||||    |     |   |  || |  | |     |||     |  ||||    |||  | ||| || |     || |||  | |||| ||||| |  | || || ||||| || |||   | ||| |||  | |||| |  || |||||||| |||||||||||||||||||||||  | | |||    |
gtatatctacttctgttctggtagcttttcaatttgtttgcacttctgttgttctttcaatcaagaccttattgttgatattcaggcttttccttttccctgttccctttccatatcagttattat-ctggtcataatgtttctttctaattgc-agGTTACCACACGGTCACCAAAAGATGGAATATGTTATAAGAAGTTGCCAAGATCAAGTGCTATTAAGGTGATTGATTTTGGTAGCACAGCTTTTGAGTGTC

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|45568628|gb|CK986157.1|CK986157
EST:     CCTTGTTTCTCCGGAGTACATTAAAGTGCCTGAATACAAA                         GTCTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: CCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
EST: gi|76015337|gb|DT942507.1|DT942507
EST:     AGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA                         GTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: AGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
EST: gi|211429794|gb|FL437778.1|FL437778
EST:     AGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA                         GTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG
genomic: AGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAG

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), 48 (downstream exon)
Score: 139

TTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

TTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

TTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 174

TTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttg ... catttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC
                           tactgat  putative branch site (score: 174)
                                 tcctctttttttcatt  CT-rich tract
           tgaatattgaatat  TA-rich tract