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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgcagcccgtggtactctatacttacaccattcgccagtcaaaccgctaacgtgcaaattttgcccatggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG

Basic information

species Zea mays
transcript AC217947.4_FGT002
intron # 13
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 13
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 13
gtttgttgcagcccg-tggta-ctctatacttacacc---attcgcca-gtcaaaccgctaacgtgcaaattttgcccatggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG
|||| |||| |  |  || ||  | || |     ||    |||    | |  ||    ||||  |  ||||      |||| |  ||||| || ||  |||||||| |||| ||||||||||||||||| || || ||||||||||||||||||||||||||||||
gtttcttgctgttcaatgataattttacatcactactgatatttattatgagaagtaactaatatataaatgc-attcatgatatcagGAGAGGCTGTCTCAAAAACAATCAGGAGCTGAGCTTGGTCGCTCCGTATTCTTCTTTGGATGCAGAAACAGCAAGATG
















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|92087911|gb|EB484142.1|EB484142
EST:     TCATGATTGGCCCTGGGACCGGTCTTGCACCCTACCGTGGCTTCTTGCAG                         GAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
genomic: TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
EST: gi|211060797|gb|FL421770.1|FL421770
EST:     TCATGATTGGCCCTGGGACCGGTCTTGCACCCTACCGTGGCTTCTTGCAG                         GAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
genomic: TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
EST: gi|76932021|gb|DV172915.1|DV172915
EST:     TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAG                         GAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
genomic: TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
EST: gi|32842091|gb|CD981772.1|CD981772
EST:     TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAG                         GAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
genomic: TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
EST: gi|32842090|gb|CD981771.1|CD981771
EST:     TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAG                         GAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC
genomic: TCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTC

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), 49 (downstream exon)
Score: 134

TGTGAGGCAATCAAACTTCAAACTACCCGCTGATCCTTCAGTACCGATTATCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 439

TGTGAGGCAATCAAACTTCAAACTACCCGCTGATCCTTCAGTACCGATTATCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

TGTGAGGCAATCAAACTTCAAACTACCCGCTGATCCTTCAGTACCGATTATCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 484

TGTGAGGCAATCAAACTTCAAACTACCCGCTGATCCTTCAGTACCGATTATCATGATTGGCCCTGGGACCGGTCTTGCACCCTTCCGTGGCTTCTTGCAGgtttgttgca ... atggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacaccattcgccagtcaaaccgctaacgtgcaaattttgcccatggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG
                                  aaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgcagcccgtggtactctatacttacaccattcgccagtcaaaccgctaacgtgcaaattttgcccatggtcccagGAAAGACTTGCTCAAAAAGAATCTGGAGCTGAGCTTGGTCGATCTGTGTTCTTCTTTGGATGCAGAAACAGCAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG