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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtgtcttgggtgcatatgggtgtatgggaaggagattactttaggtaggactatttctataagtttaccttgggatggttttgagtggacttcctattgctttcaaaacggctctccatttccatttctggattatacttgatatcatctgcacttcactgtgggcctcatctttctgtag

Basic information

species Zea mays
transcript GRMZM2G128121_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 9
TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtgtcttgggtgcatatgggtgtatgggaaggagattactttaggtaggactatttctataagtttaccttgggatggttttgagtggacttcctat------------tgctttcaaaacggctctccatttccatttctggattatact---tgatatcatctgcacttcactgtgggcctcatctttctgtag
 ||||||||||| |||||  ||||||||||||||||||||||||||||    || || ||||||||||| ||||||||||||    | | ||  ||    ||| |||||| || |     ||   ||| | ||  |  || | || ||   ||  |   ||| | || ||  | | |            ||  | | | |    |    || |  |||||||   || | |   |||  |    || ||||  ||||||| ||  ||| |||||||
CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgtac--tagctgtgtacacatgtttgggaaagaaacatacttgcatagaattaccttgattatttcaca--ggagtcccttttaatgaacaccttgttttctagataagtgtataccagatacatgctgatatatatttctgttatacagtcagtgaagtttgatgtacttacctgtgggtct--tctctctgtag
















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|78104220|gb|DV522638.1|DV522638
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|71325375|gb|DR799361.1|DR799361
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|93013442|gb|EB638962.1|EB638962
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|71331066|gb|DR802363.1|DR802363
EST:     AGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: AGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|211386006|gb|FL329690.1|FL329690
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCAATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|211417439|gb|FL345693.1|FL345693
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|149109553|gb|EE293365.2|EE293365
EST:     AGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: AGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|4730273|gb|AI649439.1|AI649439
EST:     TGCTGAAGTGC-TGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: TGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|78081841|gb|DV510253.1|DV510253
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|78180140|gb|DV550513.1|DV550513
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|12045820|gb|BF727959.1|BF727959
EST:     TGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGTATTAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGT
genomic: TGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCA-AAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGT
EST: gi|31348876|gb|CD433233.1|CD433233
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|76290822|gb|DV030390.1|DV030390
EST:     TGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: TGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|76021492|gb|DT948662.1|DT948662
EST:     AGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: AGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
EST: gi|6859967|gb|AW355961.1|AW355961
EST:     CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG                         ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTT

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: 48 (upstream exon), 39 (downstream exon)
Score: 184

TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 223

TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 437

TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtg ... ctttctgtagATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtgtcttgggtgcatatgggtgtatgggaaggagattactttaggtaggactatttctataagtttaccttgggatggttttgagtggacttcctattgctttcaaaacggctctccatttccatttctggattatacttgatatcatctgcacttcactgtgggcctcatctttctgtag

- - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG