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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG

Basic information

species Zea mays
transcript GRMZM2G029135_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 5
tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttatt---atctggtcttttcttacattgattttt--cagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
      |||||| | ||   |    ||   |||   |  | ||   |    |  ||   |   |   | |   ||   ||  | ||||  ||  | ||||  ||||| ||||| ||  |||||||||| ||||||||||| || ||| | ||||||||||||||||||||||| |||||| ||||||||||||||||||||||||
-----cttacttttctgtatgactgcttcacctaaaccttgtttaccaactaggttagccaaataaaagtcaaataaagtgatgtcttctatcaaattttggcagGCCTTTGTAAATGTGGTCCTCACCCTTTGTGATGCTGGGGATGCAGTTGTCATGTTTGCACCATATTACTTCAATTCCTACATGTCATTCCAGATGACAG

upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G43830.1 (Glycine max), 3'ss of exon 4
--tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatct---tgtct-tattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
    |||||  ||| | || |      || |    || |     || |  ||  |     |||     ||| |  || || || ||||| ||||       | ||||| ||||||||  | || || ||||| |||||| | |||||||| || || |||||||| || || || ||||||||||||||||| ||||||||||| |
tactttgatctctt-tctgagtttgagctttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttttttcctaca-----aatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCCGTGGTTATGTTTGCTCCTTACTACTTCAATGCCTACATGTCCTTCCAGATGACTG

upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G01520.2 (Glycine max), 3'ss of exon 1
-tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
   |||||  ||| | || |     ||| |    || |     || |  ||  |     |||   | | |    |    | || |     |     | ||||| ||||||||  | || || ||||| |||||| | ||||||||||| || |||||||| || || || |||||||| |||||||| ||||||||||| |
actttgatctctt-tctgagtttgaactttcaagtttcaacagtattattgtgctcatctctaaacatctgtggtaacttgttgtattcctacaaatacagGCATTTGTGAATCTAGTTCTTACTCTCTGTGATCCGGGTGATTCTGTGGTTATGTTTGCTCCTTACTACTTCAATGCGTACATGTCCTTCCAGATGACTG

upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G80360.1 (Arabidopsis thaliana), 3'ss of exon 5
tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttattatctggtctt-ttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
     || || | | |  |   || || ||  || |   | || || |||    ||  |||  ||| ||  |||| |  | || || |||  | | |  |||| ||||||||| | ||  | ||  | |||||||| |||||||| |||||||||||||  ||||| || |||||  |||||||| | || ||||||||||
---gtataacctgtctttgtttactcttttgattgc---tcttccttctg--ttttcttctactctcatactctgtttctgtttttgcatctaatgt--agGCGTTTGTGAACCTTGTTATTACATTATGTGATGCTGGTGATTCGGTTGTCATGTTTGAGCCATACTACTTCAACTCCTACATGGCCTTTCAGATGACAG

upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 4
tgttgattacttctttgggggcacactcttcctttcctgtttta-ctcctgaaccttgatcttgtcttattatctggtcttttcttacattgattttt--cagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
| | ||  | ||  |   |  |   || ||        || ||| || |    | ||  ||| | ||| | |     | | | ||||  ||  ||  |  ||||| ||||||||  | || || ||  | |||||||| || ||||  ||||| |||||||||||||| || |||||||| |||||||| |||||||||||||
tatagaacagtttct---gttcttgctattagccaaaagtgttagcttccatccatttttctagacttctaaagcattgtctacttattttacttgatggcagGCATTTGTGAATCTCGTTCTTACATTATGTGATGCTGGAGATTTGGTTGTTATGTTTGCACCATACTACTTCAATGCATACATGTCCTTCCAGATGACAG

upper sequence: GRMZM2G029135_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17703 (Selaginella moellendorffii), 3'ss of exon 4
tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
                                        |  |||   | |   |    ||   |    || |  | || |  |   ||  | |  ||||| | || ||| || |  |||| | | |||||| | || ||||| || || |||||||| |||||||| |||||||| |||| | ||||||||||||| |
---------------------------------------gtgaactaacgcaatcttccgttccataggcatttattgttctagtgattttttctcccagGCCTATGCGAATTTAGCACTCAGTTTGTGTGATCCAGGAGATTCCGTGGTAATGTTTGCTCCATATTACTTCAATGCGTACACGACATTCCAGATGACTG

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|71772847|gb|DR970770.1|DR970770
EST:     AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAA                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
genomic: AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
EST: gi|148944112|gb|EC889198.2|EC889198
EST:     AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAA                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
genomic: AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
EST: gi|71444321|gb|DR825371.1|DR825371
EST:     AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAA                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
genomic: AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
EST: gi|149102126|gb|EE287567.2|EE287567
EST:     AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAA                         GCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC
genomic: AGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTC

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: 44 (upstream exon), 49 (downstream exon)
Score: 72

TTACGCAGAGAGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

TTACGCAGAGAGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

TTACGCAGAGAGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 213

TTACGCAGAGAGAATAAGCTTACTAAGTCATCAGTTATGGTCACTGCTGGTGCAAATCAAgtaaaaactt ... gatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgaaccttgatcttgtcttattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG
                                               tttttc  CT-rich tract
                                      ttacattgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgattacttctttgggggcacactcttcctttcctgttttactcctgaaccttgatcttgtcttattatctggtcttttcttacattgatttttcagGCTTTTGTGAACTTGGTCCTCACTCTTTGTGATGCCGGTGATTCTGTTGTCATGTTTGCACCATATTATTTCAATGCCTACATGTCATTCCAGATGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
tgttgat
- - - - - - - - - - gcacact
- - - - - - - - - - - - - - - - - - ctgtttt
- - - - - - - - - - - - - - - - - - - - - - - -ctgaacc