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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggactcttgttttttctttatgtttaatgtagattacctttgtttggatgatgcataattcatcaaatgtaatgccaatcttatctatcaacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG

Basic information

species Zea mays
transcript GRMZM5G860137_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860137_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g02020.1 (Oryza sativa), 3'ss of exon 7
ttggactcttgttttttctttatgtttaatgtagattacct--ttgtttggatgatgcataatt-catcaaatgtaatgccaatcttatctatc------aacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG
         | | | |  ||||   | ||  ||   ||  |   |||||   |||||  | | |  |    |  |     |  |||  | || |      ||  | ||||||||| ||||||||||| || || ||||||||| |||||||||||| |||||||||| |||||||||||||||| | ||||||||| |||||||| |||
---------tttctctagtttaaagtcaaattatgctatatgcatgtttacttgatgtgtgactgtagtgcacctctcttccttctcgtttaccttccaaaattcgcagTGATGGTGCTGCTGCAATCGTGCTAGTCAGTGGACAGAAAGCCAAGAGTCTTGGCCTTCAAGTTATTGCAAGGATCAGAGGGTATGCGGATGCTGCTCAG
















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|78180536|gb|DV551029.1|DV551029
EST:     ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAGAGCCAAGAATCT
genomic: ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|71426142|gb|DR807192.1|DR807192
EST:     ACTTTTAAGACGAAGGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
genomic: ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|93281947|gb|EB674211.1|EB674211
EST:     TGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
genomic: TGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|149110542|gb|EE294180.2|EE294180
EST:     ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
genomic: ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|110202377|gb|EC884274.1|EC884274
EST:     TGGCAATTTC-TCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
genomic: TGGCAA-TTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|71298332|gb|DR785147.1|DR785147
EST:     ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAGAGCCAAGAATCT
genomic: ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|6994169|gb|AW453383.1|AW453383
EST:     ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAGAGCCAAGAATCT
genomic: ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|12047245|gb|BF729384.1|BF729384
EST:     ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAGAGCCAAGAATCT
genomic: ACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
EST: gi|110939957|gb|EE160114.1|EE160114
EST:     GACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG                         TGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT
genomic: GACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCT

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), 40 (downstream exon)
Score: 42

TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 171

TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG


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

TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 55

TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAGgtttgtttcc ... caacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatgatgcataattcatcaaatgtaatgccaatcttatctatcaacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG
           ataattcatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggactcttgttttttctttatgtttaatgtagattacctttgtttggatgatgcataattcatcaaatgtaatgccaatcttatctatcaacacacagTGATGGCGCTGCTGCAATTGTCCTTGTCAGTGGAGAGAAAGCCAAGAATCTTGGCCTTGAAGTTATTGCAAGGATTACAGGGTATGCTGATGCTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - -tgttttt
- - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - atgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcca