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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcttccattcttttttatgatatcttttgtcactcatcagcttttagactaaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG

Basic information

species Zea mays
transcript GRMZM2G164265_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 6
--------gtaagtatcttccattcttttttatgatatcttttgtcactcatca-----gcttttagactaaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG
         ||  | | | |||||| ||  | |  |  ||  |||  |||||||     | || |  | |||| |    ||| ||| | ||||||||| ||||| |||||| |||||||||||||||||||  ||| || ||||||||||||||||||||||||||
gtaagcacctagatttatcccattcattgctgt--tgcctcgtgttcctcatcatttgtgtttatgtattaaaagtaataac-atcattaacagGATGTCTCCACATATGGGTGCTTGCATTGCTGTAGAGGCCATTTCAATTCTTGAGAAGCTCCATTCTAAAGG

upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 6
-----------------------gtaagtatc--ttccattcttttttatgatatcttttgtcactcatcagcttttagactaaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG
                       || |||||   |||  || |  |   ||  || | ||   |||| ||   | | || |  | |          |  |  |||| ||| | |||||||||| ||| |||||||| ||||||   ||||| ||||||||||||||||| |  |||||
gtaagatttgtaccctcccttttgttagtataggttcacttttaatagctgcaatttatttaaactcttcctatataagccccattaacattttagttctggacagAATGTCACCAAATATGGTTGCGTGCATTGCAGTAGAGGCAATATCAATTCTTGAGAAGCTCCACTTGAAAGG

upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 6
------------gtaagtatcttccattcttttttatg-atat-cttttgtcactcatcagcttttagact------aaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG
             |   | |||  |  ||| | | |   | |  |       | |   ||  ||||   ||      || |  |  || |   |||| ||||||| | ||||||||||  ||||||||||| ||||||   ||||| ||||| |||||||| ||    || ||
gtaagaaatagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaa-cagGATGTCACCAAATATGGTGGCTTGCATTGCAGTAGAGGCAATATCAATTCTCGAGAAGCTTCACATGAAGGG

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|67020152|gb|CO448901.1|CO448901
EST:     GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC                         GATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
genomic: GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
EST: gi|9952315|gb|BE638898.1|BE638898
EST:     GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC                         GATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
genomic: GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
EST: gi|18654924|gb|BM499729.1|BM499729
EST:     GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC                         GATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
genomic: GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
EST: gi|18661950|gb|BM501665.1|BM501665
EST:     GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC                         GATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
genomic: GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
EST: gi|7145135|gb|AW506616.1|AW506616
EST:     ATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC                         GATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
genomic: ATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
EST: gi|71430775|gb|DR811825.1|DR811825
EST:     GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGC                         GATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT
genomic: GATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCT

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: 151

GTAATGGATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 144

GTAATGGATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GTAATGGATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

GTAATGGATATGCTTGGTCCCAGCCTTTGGGACGTGTGGAATTCAATGGGGCAGGCgtaagtatct ... tcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcttttgtcactcatcagcttttagactaaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG
                           gactaaa  putative branch site (score: 77)
                      ttttaga  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcttccattcttttttatgatatcttttgtcactcatcagcttttagactaaatggtccaactatcgtaaacagGATGACTCCAAATATGGCTGCTTGCATTGCTGTAGAGAGCATATCGATTCTTGAGAAGCTCCATTCTAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC