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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttgttttaccgaaatcacaactctagacatagccgcaaaaaatcaagttttttttttcactatcagcaaggcatgttgatgcaatgatattttttctgttgctatatctgaatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 3'ss of exon 5
gtatgttttgttttaccgaaatcacaactctagacatagccgcaaaaaatcaagttttttttttcactatcagcaaggcatgttgatgcaatgatattttttctgttgctatatctgaatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG
||| ||| | | |  || |   |||| || |  |  ||||    ||   | |  | ||||   || |  |  ||    |||  |||| || |  | |    |   ||| ||| | |  |||||| ||||||||||||||||||||||||||||||||||||| || ||||| |||| |||  ||||||||||| |||| || |||||||| || ||||||||||||
gtaagttctttct--ccaagtgcacagctgtgaatttagctatgaatt-ttacttgttttgcatcccagtttgct---cat-ctgatacattactctaacatgctttg-tatctgtttatgtac-agCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGTATTCGCTCTATGAATCAGGAACCACATATATGTGCAACATGGGGAGACACAGGTCATGTTCAG

upper sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g03822.1 (Oryza sativa), 3'ss of exon 5
gtatgttttgttttaccgaaatcacaactctagacatagccgcaaaaaat-caagttttttttttcactatcagcaaggcatgttgatgcaatgatattttttctgttgctatatctgaatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG
||| ||| | | |  || |   |||| || |  |  ||||    ||   | |  |||||   |  || | |     |    |     | |  | | ||  ||| |||     | | || |||||| || |||||||||||||||||||||||||||||||||| || ||||| |||| |||  ||||||||||| |||| || |||||||| || ||||||||||||
gtaagttctttct--ccaagtgcacagctgtgaatttagctatgaattttacttgttttgcatcccagt-ttgctcatttgttacattactctaacatgctttgtgtc----tgtatgcatgtac-agTTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGTATTCGCTCTATGAATCAGGAACCACATATATGTGCAACATGGGGAGACACAGGTCATGTTCAG
















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|78089597|gb|DV517971.1|DV517971
EST:     GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACAT                         CTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
genomic: GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
EST: gi|19822069|gb|BQ048093.1|BQ048093
EST:     GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACAT                         CTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
genomic: GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
EST: gi|31349324|gb|CD433681.1|CD433681
EST:     GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACAT                         CTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
genomic: GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
EST: gi|31350283|gb|CD434640.1|CD434640
EST:     GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACAT                         CTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
genomic: GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACT
EST: gi|26457087|gb|CA828670.1|CA828670
EST:     GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACAT                         CTAAAAAAGGTGGCTCATGCGG
genomic: GCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGG

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: 45 (upstream exon), 49 (downstream exon)
Score: 133

ACCAGCTTCAGCAGTTGAAGCTGACACTGATGTGGATAGTGACAGCAGCAGCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 112

ACCAGCTTCAGCAGTTGAAGCTGACACTGATGTGGATAGTGACAGCAGCAGCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

ACCAGCTTCAGCAGTTGAAGCTGACACTGATGTGGATAGTGACAGCAGCAGCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

ACCAGCTTCAGCAGTTGAAGCTGACACTGATGTGGATAGTGACAGCAGCAGCGATGAAGAAGATGAAGAGATTAATGAGGATACAAAACCCATCCTACATgtatgttttg ... aatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaggcatgttgatgcaatgatattttttctgttgctatatctgaatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG
        tgttgat  putative branch site (score: 98)
                 aatgatattttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttttgttttaccgaaatcacaactctagacatagccgcaaaaaatcaagttttttttttcactatcagcaaggcatgttgatgcaatgatattttttctgttgctatatctgaatgtaccagCTAAAAAAGGTGGCTCATGCGGGGTGTGTAAATCGGATACGCTCAATGACTCAAAAACCACATATAAGTGCTACGTGGGGAGATACTGGTCATGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT