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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattggatgaaattgcttgattcctctttagctctactaaaatgtctctccacctaacccatgtgtctactgaagtaaaagatttttgtttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG

Basic information

species Zea mays
transcript GRMZM2G030596_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 6
-aaaattggatgaaattgcttgattcctctttagctctac-taaaatgtctctccacc-taacccatgtgtctactgaagtaaaagatttttgtttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG
   |      | |   |  |||     |||       ||  |||||| ||| |||||| |    ||| | |||| | || ||     |||||  |  ||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| || |||||||||||  |||| ||||| 
ccgatcccactaagcctttttgcccagtctggtttattatgtaaaatttctgtccaccctggttcatatatctatttaattatc---ttttttgtgtctgtagGGTGCCAACAAGAAGTATCGGTCTTCTTTCATACACATTTTTGATGGAAACTGGCTGCGATGATGTTTTGGTTCCAACA
















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|76286071|gb|DV025639.1|DV025639
EST:     ATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG                         GGTGCCAACTAGAAGTATCGGCCTTCTTTCT
genomic: ATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCT
EST: gi|78121768|gb|DV540152.1|DV540152
EST:     TGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAAACCAAA-TAACTG                         GGTGCCAACTAGAAGTATCGGGCTTCTTTCTTACACATTTTTGA
genomic: TGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAA-CCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGA
EST: gi|78111592|gb|DV529989.1|DV529989
EST:     TGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAAACCAAA-TAACTG                         GGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAAC
genomic: TGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAA-CCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAAC
EST: gi|78114931|gb|DV533319.1|DV533319
EST:     ATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG                         GGTGCCAACTAGAAGTATCGGCCTTCTTTTCT-ACACATTTTTGATGGAAA
genomic: ATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTT-CTTACACATTTTTGATGGAAA
EST: gi|78075870|gb|DV504304.1|DV504304
EST:     ATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTG                         GGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTTGATGGAAA
genomic: ATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTT-GATGGAAA

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), 47 (downstream exon)
Score: 175

ATGGCAATGGTTTCAAGACTAGTACGATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 103

ATGGCAATGGTTTCAAGACTAGTACGATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

ATGGCAATGGTTTCAAGACTAGTACGATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

ATGGCAATGGTTTCAAGACTAGTACGATGCGGCTTGGAGCAGATGTGATTGTTTTTACACAAAACCAAAATAACTGgtacttaacc ... tttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctctccacctaacccatgtgtctactgaagtaaaagatttttgtttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG
        acctaac  putative branch site (score: 96)
                                       tttttgtttcctgt  putative PPT
                                taaaagatttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattggatgaaattgcttgattcctctttagctctactaaaatgtctctccacctaacccatgtgtctactgaagtaaaagatttttgtttcctgtagGGTGCCAACTAGAAGTATCGGCCTTCTTTCTTACACATTTTTGATGGAAACAGGTTGCGATGATGTGCTGGTGCCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - ttggatg
- - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaaga