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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatttagtttgattattccttcacaagacatgattctcccaattatagatacatccatatttaaacttagtttactgattacagttttgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871336_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g05830.1 (Oryza sativa), 3'ss of exon 3
taaaatttagtttgattattc--cttcacaagacatgattctcccaattatagatacatccatatttaaacttagtttactga-ttacagttttgttat--gcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG
     | || || | ||||||    |  ||    |  || ||||  ||| ||    | | ||| | ||   | |||||  ||| ||||   ||  | ||  |||||| || |||| |||||||||||  || ||| |||| ||  |||| |||||||||||||| ||||| ||||| ||||| |||||
----ctgtaattcgcttattcgatcttgcatacaagaatgctccggattgtattagccttcatctctat-ttcagtttggtgaattactagttcatcatttgcagTTATTCGAAGTCCCTCTTGATGGGAAGGAAGTATCACTGAGATACAGCTCTGCTCTTGTCCAAGGAGCTACTAATGTTTTTTG

upper sequence: GRMZM5G871336_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g04350.t01 (Vitis vinifera), 3'ss of exon 3
--taaaatttagtttgattattccttcacaagaca-tgattctcccaattatagatacatccatatttaaacttagtttactgattacagttttgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG
      | | | |   |   ||    || | |||  |  ||||    | | | | |    | ||  |      |||  | ||  || || |||| || ||||||| ||||| |  |  |||||  |    ||| |     | || |||   ||||||||||||||||||||||||||||| || ||
atctgtaatcaatcaaaggcttttagcagatgactctttttcttttcactct-ggtgttccaatgatgttgaataggatgctt-ttgca-ttttcttttgcagTTATTTGAGGTTCAACTTGAGAATTCTGAAGTGCTCTTCCGTTATTCATCTGCTCTTGTTCAAGGTGCTACAAATGTGTTCTG
















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|71430125|gb|DR811175.1|DR811175
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211068146|gb|FL037286.1|FL037286
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211070875|gb|FL037292.1|FL037292
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211070877|gb|FL037294.1|FL037294
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGA
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGA
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|13381878|gb|BG458553.1|BG458553
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211070880|gb|FL037297.1|FL037297
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATAT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATAT
EST: gi|93012464|gb|EB637984.1|EB637984
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211073617|gb|FL037309.1|FL037309
EST:     GAGCCAGGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATTGAAAAAGAAATATCGCTACG
genomic: GAGCCAG-TCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGAT-GAAAAAGAAATATCGCTACG
EST: gi|211070874|gb|FL037291.1|FL037291
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTT
EST: gi|149059964|gb|EE157094.2|EE157094
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|149045945|gb|EE047943.2|EE047943
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211070882|gb|FL037299.1|FL037299
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211070884|gb|FL037301.1|FL037301
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCACAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCT
EST: gi|211070878|gb|FL037295.1|FL037295
EST:     GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGG                         TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATA
genomic: GGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATA

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: 46 (upstream exon), 49 (downstream exon)
Score: 50

TAGAGTGCCTGAAAGTGGCAGGCGTATACTTGAGTTGATTGTGCAACTCTGGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 19

TAGAGTGCCTGAAAGTGGCAGGCGTATACTTGAGTTGATTGTGCAACTCTGGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 20

TAGAGTGCCTGAAAGTGGCAGGCGTATACTTGAGTTGATTGTGCAACTCTGGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

TAGAGTGCCTGAAAGTGGCAGGCGTATACTTGAGTTGATTGTGCAACTCTGGAGCCAGTCCTTCGCGGCCAACATATTTGCACTTCTTTTCCAGAAATGGgtatgctgtg ... tgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagatacatccatatttaaacttagtttactgattacagttttgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG
                              tactgat  putative branch site (score: 36)
                                          ttttgtt  putative PPT
              atatttaaacttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatttagtttgattattccttcacaagacatgattctcccaattatagatacatccatatttaaacttagtttactgattacagttttgttatgcagTTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG

- - - - - - - - - - -cttcaca
- - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -acatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatt