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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttaaacatcctcttttcaatcaagagtcactgcaccagtaagcagtaaaggatatattcatctttgtaactagtttatgtttctgtgtcacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT

Basic information

species Zea mays
transcript GRMZM2G156251_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 5
lower sequence: 13113.m00244 (Oryza sativa), 3'ss of exon 7
--gcttaaacatcctc---ttttcaatcaagagtcactgcaccagtaagcagtaaaggatatattcatctttgtaactagtttatgtttctgtgtcacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAG---AAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT
      |||    |      | ||  |||  | ||  |  |   ||    |||  |  ||| ||       | |  ||    | | | |   | |     | ||| |||||||| |||||||||||||| |||||   |   |||||||||||| | || ||||||||||  ||||| |||||||| ||||| ||||||||||||   
ccatccaaatgagcctgaactgtctttcactaatctgtctaattgtttctagtgtatcatacatgatgtcatatgcctttgctgtatattcttat-----tccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAACGCGGGATCGATCTCAAAGGGCAGGACCAGCTCCAGAGGCTAATGCAGAG---

upper sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 5
gcttaaacatcctcttttcaatcaagagtcactgcaccagtaagcagtaaaggatatattcatctt--tgtaactagtttatgtttctgtgtcacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAG---AAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT
    |  ||        | ||       |||||   |     |   ||      | |||    | |  ||| |   |  | || |      ||    | ||| |||||||| |||||||||||||| |||||   |   |||||||||||| | || ||||||||||  ||||| |||||||| ||||| ||||||||||||   
--ccatccaaatgagcctgaactgtctttcactaatctgtctaattgtttctactgtatcatacatggtgtcatatgcctttgctgtatattcttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAACGCGGGATCGATCTCAAAGGGCAGGACCAGCTCCAGAGGCTAATGCAGAG---
















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|12047004|gb|BF729143.1|BF729143
EST:     CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
genomic: CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
EST: gi|31353665|gb|CD438022.1|CD438022
EST:     CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
genomic: CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
EST: gi|78180467|gb|DV550840.1|DV550840
EST:     CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
genomic: CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
EST: gi|8102733|gb|AW927375.1|AW927375
EST:     CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
genomic: CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
EST: gi|32803335|gb|CD955571.1|CD955571
EST:     TAAGGGACGAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
genomic: TAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
EST: gi|8102732|gb|AW927374.1|AW927374
EST:     CCACCAAGC-AGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
genomic: CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG
EST: gi|67028072|gb|CO456821.1|CO456821
EST:     CCACCAAGCAAGGAGATGGATGCCAAGTTAACAGACCAGGAGGCTAGAAG                         ACTACGAGCGGCTGCAAAGCCCAAGGGAGA-CAGAAAAGGACTCGAC-ACG
genomic: CCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACG

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), 47 (downstream exon)
Score: 183

TTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

TTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

TTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

TTTTTTCAACCGAGCCTTATGCTTGTAACCCTTCAAGTCTGCCAACATATCCACCAAGCAAGGAGATGGATGCCAAGTTAAGAGACGAGGAGGCTAGAAGgtgtgtcaca ... cacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaaggatatattcatctttgtaactagtttatgtttctgtgtcacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT
                    ttgtaac  putative branch site (score: 111)
                                            tcacccttc  putative PPT
        atatattcatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttaaacatcctcttttcaatcaagagtcactgcaccagtaagcagtaaaggatatattcatctttgtaactagtttatgtttctgtgtcacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAGAAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - -catcctc
- - - - - - - - - - - - - - - -ctgcacc
- - - - - - - - - - - - - - - - - - - - - agcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct