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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagaatatcttcccatatatgatgctatgtatttttgtttatattgcactgcaatatgtttgcatttctggtgtattgattttacttgtttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC

Basic information

species Zea mays
transcript GRMZM2G085474_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085474_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
tgagaatatcttcccatatatgatgctatgtatttttgtttatattgcactgcaatatgtttg-catttctggtgtattg---attttacttgtttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC----------------------
      |     |    || || ||  || | | | | | ||  ||| | | || ||| |||  ||||  |    |||     |||||| |  ||  |  ||||||||| | |||||| ||||||||  |||||||||||||||||||  ||||||||||                      
--ccggtgatcacattgatttgttgtaatatttctat-tatactttgtaataca-tatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
















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|78114650|gb|DV533038.1|DV533038
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
EST: gi|149008746|gb|EE040943.2|EE040943
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGA-GACCAG                         GATGCTTTTGC
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGC
EST: gi|211385847|gb|FL095517.1|FL095517
EST:     GTGTGCCGAACTTTGTGCTGACNATCATGCCCTCACAAGAGAAGACCCAG                         -ATGCTTTTGCTATCCAAAGCAACCAGCGTGGGAATTGCTGCTCGTGACA
genomic: GTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACC-AGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGG-AATTGCTGCTCGTGACA
EST: gi|32863231|gb|CF002913.1|CF002913
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
EST: gi|149050402|gb|EE155650.2|EE155650
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAAGCA-CCAGCGTGGAATTGCTGCTCGTGACAG
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAA-GCAACCAGCGTGGAATTGCTGCTCGTGACAG

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), 48 (downstream exon)
Score: 544

CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 206

CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 773

CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcactgcaatatgtttgcatttctggtgtattgattttacttgtttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC
                             tattgat  putative branch site (score: 773)
                                        cttgttt  putative PPT
                             tattgattttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagaatatcttcccatatatgatgctatgtatttttgtttatattgcactgcaatatgtttgcatttctggtgtattgattttacttgtttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGTGGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT