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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaatcaaactagcagatgttttcttcacaatattgtgacctgtctagtagccttatgtgcaatcttaattctcattacttgttattattttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT

Basic information

species Zea mays
transcript GRMZM2G086030_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 17
----ttcaatcaaactagcaga---tgttttcttcacaatattgtgacctgtctagtagccttatgt---gcaatcttaattctcattac-ttgttattattttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT
    |||||| ||  | |  |    | || | |   |   || ||||  ||| |  | ||   ||||   ||||    | || ||| ||   |  | || ||| |  |||||||||| ||||||| |||||||||||||||||||||||||| ||||| |||||||| || || ||||||||||||||||| |||||||||||||||||||
gtatttcaatgaatttggtgggctgtattctatctgctgcatagtgatgtgtttt-tggcacaatgtttggcaactgcatttttcactagacttctgttctttctctgtagGCAACTATATATCAGCAGAAGGCACTTGATATCAATGAAAGAGAGCTAGGTCTTGACCACCCAGAAACTATGAAGAGTTACGGGGATTTATCTGTCTTCT

upper sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 17
ttcaatcaaactagcagatgttttc--ttcacaatattgtgacctgtctagtagccttatgtgcaat--cttaattctcattacttgttattattttttggt--agGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT
     || | ||    | | |  |   ||  |  | ||||    |||||   ||      || || |  ||| ||||||   ||||    ||  ||  | ||  |||||||| ||||||||||||||||  | ||||||||||| ||||| ||||| ||||| ||||| || || ||||| || ||||| ||| | || || || |
---tttccagctgcttggtctcgttggttttctgtgttgta---tgtctgcaagtgactggtccagttgctttattctctaaacttaaattttcttccttgtctagGCAACTATATATCAACAGAAGGCTTTGGATATCAATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTT
















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|31353676|gb|CD438033.1|CD438033
EST:     TTATCATACTGGAGATTTTAATCAG                         GCAACTGTATATCAATTCA-AA-GCACTTGATATCAATGAAAGGGAGCTTG
genomic: TTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAA--CAGAAGGCACTTGATATCAATGAAAGGGAGCTTG
EST: gi|31357595|gb|CD441952.1|CD441952
EST:     CATACAGCCTTCTTGCTGTGGTGCTTTATCATACTGGAGATTTTAATCAG                         GCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGT
genomic: CATACAGCCTTCTTGCTGTGGTGCTTTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGT
EST: gi|33467411|gb|CF244460.1|CF244460
EST:     ATACAGCCTTCTTGCCTG-GGCGCTTTATCATACTGGAGATTTTAATCAG                         GCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGT
genomic: ATACAGCCTTCTTG-CTGTGGTGCTTTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGT

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), 48 (downstream exon)
Score: 149

GTCCAAAATTATAGCTGTTTGTGGTCCATACCATCGACTGACGGCTAATGCATACAGCCTTCTTGCTGTGGTGCTTTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

GTCCAAAATTATAGCTGTTTGTGGTCCATACCATCGACTGACGGCTAATGCATACAGCCTTCTTGCTGTGGTGCTTTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

GTCCAAAATTATAGCTGTTTGTGGTCCATACCATCGACTGACGGCTAATGCATACAGCCTTCTTGCTGTGGTGCTTTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 393

GTCCAAAATTATAGCTGTTTGTGGTCCATACCATCGACTGACGGCTAATGCATACAGCCTTCTTGCTGTGGTGCTTTATCATACTGGAGATTTTAATCAGgtactttaat ... tttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagtagccttatgtgcaatcttaattctcattacttgttattattttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT
                   tcttaat  putative branch site (score: 393)
                                         ttatttttt  putative PPT
                     ttaattctcattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaatcaaactagcagatgttttcttcacaatattgtgacctgtctagtagccttatgtgcaatcttaattctcattacttgttattattttttggtagGCAACTGTATATCAACAGAAGGCACTTGATATCAATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- -aatcaaa
- - - - - - -gcagatg
- - - - - - - - - - - - cttcaca
- - - - - - - - - - - - - - - - - - -tgacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtgc