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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataaattcataatcaatcttgttcaattgggcacgagcaatattttggcatttcttgtagtactattgagtaaaacatggtttttatttgtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG

Basic information

species Zea mays
transcript GRMZM5G868168_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868168_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 7
cataaattcataatcaatcttgttcaattgggcacgagcaatattttggcatttcttgtag---tactattgagtaaaacatg--gtttttatttgtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG
      |      | |     | | ||  |   |   | | | || |     | |||||     ||  || || | | | ||    |    ||  || |||| |||| ||||||||||| |||||||| || ||||||||||| |||||||||||||| |||||||| ||||| |||||||  ||||||||||||||   | | |
-----gtattagcttacataggatgaaaggattatcggtatttttctactcatacttgtgattttaacatagacttagatatattatcaccatcggtctgtgcagGGCGTTGAAGATCGAATGCCATCTGAATTGTCTGGTGGCATGAAAAAGCGTGTAGCTCTAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAG
















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|149004790|gb|EE039293.2|EE039293
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
EST: gi|78120174|gb|DV538558.1|DV538558
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
EST: gi|31350150|gb|CD434507.1|CD434507
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
EST: gi|33467141|gb|CF244190.1|CF244190
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTG
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTG
EST: gi|78103984|gb|DV522402.1|DV522402
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAA-GCGT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
EST: gi|154130463|gb|EC872173.2|EC872173
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
EST: gi|76931706|gb|DV172823.1|DV172823
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTG
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTG
EST: gi|148986921|gb|EE030732.2|EE030732
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCT
EST: gi|31356046|gb|CD440403.1|CD440403
EST:     ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAG                         GGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT
genomic: ACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGT

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), 49 (downstream exon)
Score: 54

ATATGAAAATTCAAGCTTACCCGAGGACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 130

ATATGAAAATTCAAGCTTACCCGAGGACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

ATATGAAAATTCAAGCTTACCCGAGGACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ATATGAAAATTCAAGCTTACCCGAGGACCGCATTGGTAAATTGGTGACAGAAACTTTGGCTGCAGTAGGACTAAAGgtaagtcaag ... gtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcatttcttgtagtactattgagtaaaacatggtttttatttgtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG
                                    tttttatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataaattcataatcaatcttgttcaattgggcacgagcaatattttggcatttcttgtagtactattgagtaaaacatggtttttatttgtgtgtgtagGGTGTTGAAGATCGTATGCCATCCGAGTTGTCTGGTGGAATGAAAAAGCGTGTTGCTCTAGCACGTTCGATAATATTTGATGATACAAAGGATGTAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - cacgagc
- - - - - - - - - - - - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaaca