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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatactttgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA

Basic information

species Zea mays
transcript GRMZM2G026231_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------gtgatactttgtttgcagacaaccagaaactttctagtttctatt-----cagctgtatcttc----ccttttaactaactatt-agaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
                                                      | |   ||  ||      ||    |||  |  || ||   |        ||||| ||| ||     |||||    |  | || | |  | || |  ||| | || |||||| || |||||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||| |
gtaatattttcccactccaaagaaaaaaaaactatgcgtaacatgcagctctcagcttgcttacttatgtgaaagagaaaaaatgttaattgtaacaacagggagctgaatcgtcttgttctttttgaaagttgttcaaaggttctgacttctatgcaaatttctaatgttcagATTCATTGGTTCTCCATTTTCAATTCTTTCATGATGGTTATTTTCCTCACTGGTTTGGTTTCAATGATATTGATGCGGACATTGAGAAATGACTATGCAA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 6
--------------------gtgatactttgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaactattag-aaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
                     ||| |   ||||            |  | || |||   | |||||| |  | |    |||   |  |  || | |   | |  |  ||||  ||  | ||  |  |    ||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||| ||||| || |||||||||||||| ||| |||||||||| ||||| |
gtacaactttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgcta---tgtattcatccatgttggtcctaccatatctctgtcactgagtattttgctcc-tttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 6
-------------gtgata-ctttgt-ttgcagacaaccagaaactttctagtttctattcagctgtatcttc---ccttttaactaactattagaaatccta-------agctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
              || || |||||| ||  |||           ||| | |||  |   | ||| | | |||   | | |  |     | ||||  ||   |       | || || ||   |||    | |  |||||||||||||||||||||| || ||||| |||||||| || ||||| ||||| ||||| || |||||||| ||||| || ||||||||||| ||||| |
gtgaaaatcattgctgctagctttgtattttagattgaagaggtgtttattgttggttacctgctatgtgttcagtcatgtggatcctatcttagccatgtcactgagagaactttgatc-cgttttctttctgtagATTCACTGGTTCTCCATTTTTAATTCTTTTATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACATTGAGAAATGACTATGCAA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 6
---------------gtgatactttgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaac---tattagaaatccta-------agctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
               |  | | ||   ||  |||           ||| | |||  |   | |||   | |||  |  |    | |   | ||||  ||   |       | || || |||| |||||  | |  |||||||||||||||||||||| || ||||| |||||||| || ||||| ||||| ||||| || |||||||| ||||| || ||||||||||| ||||| |
gtgaaaatcattgctgctagatttgtattttagattgaagaggtgtttattgttggttacctgctacgtgttcattcatgtggatcctatcttagccatgtcactgagcgaactttgatcatttttctt-tctgtagATTCACTGGTTCTCCATTTTTAATTCTTTTATGATGGTCATCTTCCTTACTGGATTGGTGTCAATGATATTAATGCGAACGTTGAGAAATGACTATGCAA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 6
--------------------gtgatactttgtttgcagacaaccagaaactttcta-gtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
                     ||| |   ||||            |  | || ||| || |  || ||  |   || | || |    ||  | | |   |||  |  ||||  ||  | ||  |  |    ||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||||||||| || |||||||||||||| ||| |||||||||| ||||| |
gtacagctttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatagctctg-ccactgagaatttt--gctcc-tttgttttctttttccctagATTCATTGGTTCTCCATTTTTAACTCTTTCATGATGGTCATCTTCCTTACTGGTTTGGTGTCAATGATATTGATGCGAACTCTGAGAAATGACTATGCAA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgatactt-tgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
   ||| || |  || ||   | | |  ||  |||||  ||| ||           |||  ||  | ||   ||| ||   ||  |   | ||||| |        ||| ||||| |||||||||||||| || ||||| |||||||||||||||||||| || |||||||| || |||||||||||| ||||| | |||||||||||||| |
---ataattattcttccaagaatctaccaaagttctatattccatctcttcaagatttctgttcaagct--ttataagccttctgagagtttgttctt--------tttgcagATCCACTGGTTCTCCATCTTTAACTCGTTCATGATGGTTATTTTCCTCACCGGTTTGGTCTCAATGATATTGATGAGGACTCTCAGAAATGATTATGCGA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 6
gtgatactttgtttgcagacaaccagaaactttcta-gtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcatttt-cagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
            ||   ||    |  | | ||| || |  |  | | | ||   | |   | |||||  ||||   | | ||  | || | ||     |||   || | | |||||||| |||||||||||||| || ||||||||||||||||| ||||| ||||||||||| || ||||| || ||||| ||  | |||||||| ||||| |
------------ttaaggattgtcttatattttatatgaattcaataatcttattttgttcatttaataaacttccacatat--tgagttgtgaatgcattctgcaatgtgcagATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACTGGTTTGGTGTCAATGATCTTAATGCGAACCCTTAGAAATGACTATGCTA

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 6
gtgatactttgtttgcagacaaccagaaactttctagtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
 || ||    |  | |    ||  | ||| ||  |     ||| |    |  || ||   |||  | |  | | |     | ||||||    || |  ||       | ||||| || |||||||| || ||||| || |||||||||||||||||||| ||||| ||||| || |||||||| ||||| ||| |  |||||||||||||||
-tgctaggaggaattccattaatgaaaaatttcatg----ctacttcatttgatattgtttttgtatt--ccagtgctttttctaagcaagctttaacttg-----gtgcagATCCATTGGTTCTCAATCTTCAATTCATTCATGATGGTTATTTTCCTCACTGGATTGGTGTCTATGATATTAATGCGAACTCTTCGAAATGATTATGCCA

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|31354711|gb|CD439068.1|CD439068
EST:     TTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAG                         ATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACT
genomic: TTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatacttt ... tcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACT
EST: gi|31355875|gb|CD440232.1|CD440232
EST:     TTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAG                         ATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCCTA-C
genomic: TTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatacttt ... tcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCC-TAAC

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: 411

GAAACTGGAAATGACATATTCAGTGAAGTGGGTAGCAACAGATGTGTCATTTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatacttt ... tcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 419

GAAACTGGAAATGACATATTCAGTGAAGTGGGTAGCAACAGATGTGTCATTTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatacttt ... tcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 492

GAAACTGGAAATGACATATTCAGTGAAGTGGGTAGCAACAGATGTGTCATTTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatacttt ... tcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 672

GAAACTGGAAATGACATATTCAGTGAAGTGGGTAGCAACAGATGTGTCATTTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatacttt ... tcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttttaactaactattagaaatcctaagctctgttcatatttctcattttcagATTCACTGGTTCTCCATTTTCAACTCTTTCATGATGGTTATTTTCCTAACTGGTTTGGTTTCGATGATATTGATGCGGACTTTGAGAAATGATTATGCCA
       aactaac  putative branch site (score: 672)
                                       tatttctcattttc  putative PPT
     ttaactaactatta  TA-rich tract