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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatattctggtttcttttgagctctttttttttgacatttgactgcttcagtgttatttacgttgcttttctgaactctgatgtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT

Basic information

species Zea mays
transcript AC217947.4_FGT002
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 6
gtacatattctggt-ttcttttgagctcttttt------ttttgacatttgactgcttcagtgttatttacgttgcttttctgaactctgatgtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT
||||  ||| |  |  |||||  ||||  ||||      ||| | |||||  | ||    |||||| |||| || | |||||||||| | |  | |    ||||||||| ||||||||||||| ||||||   ||||||||||||||||||||||  ||  ||||| |||| ||||||||||| ||||||||||||||||||
gtacgcattatcttgctctttcaagcttattttagttattttaggcattt--ccgcacttgtgttacttacatt-cctttctgaacttttacatatcaccagGAAAGAAACTCTCTGGCCAGAATTGGATCAGTTACTTCGGGATGAAAATGATGTTTCAACAGGCACTACCTACACAGCTGCCATTCCTGAATACCGGGTT
















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|108953570|gb|EC364784.1|EC364784
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATCGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|148961292|gb|EE012017.2|EE012017
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|31441089|gb|CD510520.1|CD510520
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|38502682|gb|CF972542.1|CF972542
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATCGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|28910222|gb|CB331332.1|CB331332
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|74235808|gb|DT643722.1|DT643722
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|13149591|gb|BG319913.1|BG319913
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATCGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
EST: gi|74235807|gb|DT643721.1|DT643721
EST:     GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG                         GAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA
genomic: GTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGA

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: 46 (upstream exon), 49 (downstream exon)
Score: 106

GTGGAAAGCGCCTTGTTCCAGTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 348

GTGGAAAGCGCCTTGTTCCAGTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 295

GTGGAAAGCGCCTTGTTCCAGTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 458

GTGGAAAGCGCCTTGTTCCAGTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtacatattc ... gtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgactgcttcagtgttatttacgttgcttttctgaactctgatgtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT
                                      ctctgat  putative branch site (score: 458)
                                              tgttctt  CT-rich tract
              tgttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatattctggtttcttttgagctctttttttttgacatttgactgcttcagtgttatttacgttgcttttctgaactctgatgtgttcttagGAAAGAAGCTCTCTGGCCAGAGTTGGATAGATTACTTCGGGATGAAAATGATGCCTCTCCAGGCCCTACATACACAGCTGCAATTCCTGAATACCGGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC