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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatgtgcagaatgtattagctaatagttcatatttattttctatacacacataacaattcattttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 12
-----------------gtatgtcatgtgcagaatgtattagctaatagttcatatttattttctatacacacataac--aattcattttgtg---cagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC
                   |  ||||  ||| | | | | |   ||   |  |||  |  | |  |     | || ||  | || | ||  |     ||||| | || | |||| | || |||||  |||||||||| || ||||| || |||||||| |||||||||||||| || || || |||||||| || || |
gtaagtgctggctccaaagaattcattggcatagtatctgaaaaaaatttctataccttctgttcaacagtaaatgacttactttaattcttaatttagGTTCTAAGGTATCTACTTTCGAATGCACGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACACATC

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 12
-----------------gtatgtcatgtgcagaatgtattagctaatagttcatatttattttctatacacacataac--aattcattttgtg---cagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC
                   |  ||||  ||| | | | | |   |||  | | ||  |  | |  |     |  | ||  | || | ||  |     ||||| | || | |||| | || ||| | ||||||||||| || ||||| || |||||||| |||||||||||||| || || || |||||||| ||||| |
gtaagtgctggctccaaagaattcattggcatagtttctgacaaaattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttagGTTCTAAGGTATCTACTCTCGAATTCAAGATGGTGGCTGGATGAATACAAGTTTGATGGATTTCGATTTGATGGTGTTACATCAATGATGTACACTCATC

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------------------------gtatgtcatgtgcagaatgtattagctaatagttcatatttattttctatacacacataacaattcattttgtgc--agGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC
                                         | | | | |  |   |      | |||  | ||| || | |  |   | |  |   |       || || |||    ||||  | || | |||  | || || |||||||||||||| |||||||| || |||||||||||  |||||||||| ||||| ||||||||||| ||||| |
gtatgtctctttccgtagagttgatattgcaatatttatgggaaagcctttagtgtagccccat-gctggtggtt-atgtctggtccttgtgtattgacgtttggtccttgtgtatttagGTGCTTAGGTATCTTCTTTCCAACGCGAGATGGTGGCTGGAAGAATACAAGTTTGATGGGTTCAGATTTGATGGTGTGACTTCCATGATGTACACTCATC

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 12
----gtatgtcatgtgcagaatgtattagctaat--agttcatatttattttctatacacaca--------taacaattcattttgt---------gcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC
    |||  |  |  |   | | || | |  |||  |||  | ||  |  |||  ||  |||          |||| |   |||||           ||||| ||  ||| |||  | ||||||||  | |||||||| |||||||| || |||||||| ||| |||||||||| || ||||| |||||||||||||| |
gtatgtaactttttcgtgaattttaatcgaaaatgtagtgaacatacaacttccttaagcactatcagttccaacagtctcttttgatcttttctaacagGTATTACGATATCTCCTTTCAAATGCACGGTGGTGGCTAGAAGAATACAAGTTTGATGGATTTAGATTTGATGGTGTAACCTCAATGATGTATACTCATC

upper sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 12
----------------gtatgtcatgtgcagaatgtattagctaata-gttcatatttattttctatacacacat-aacaattcattttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC
                  | ||       | | ||| ||  |   || | || ||||  ||||   |  |   || ||   |   |||  |  ||||  ||||||| ||  | |||||||| ||||||||||| || || || || ||||| |||||  |||||||||| ||||| ||||||||||| || ||||
gtatgtgctttgatgccaaagttcaagaaatagtgttttgccctttatgctcttattgttttttgttgtagggattaattgtctctttgttttagGTACTGAGATTCCTTCTTTCAAATGCAAGATGGTGGCTAGATGAGTACAAGTTTGACGGGTTCAGATTTGATGGTGTGACTTCCATGATGTACACACACC

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|67035192|gb|CO463725.1|CO463725
EST:     GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAA                         GTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA
genomic: GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA
EST: gi|101386689|gb|EB815361.1|EB815361
EST:     GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAA                         GTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA
genomic: GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA

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: 536

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC


Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 6

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctaatagttcatatttattttctatacacacataacaattcattttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC
                                acataac  putative branch site (score: 204)
                                         ttcatttt  putative PPT
     aatagttcatatttat  TA-rich tract