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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccccgcaggtcgagtttttttaataattcctattattattgttttggggatgcaccatgccaccacagtttatgaagcatttgtcttggtgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG

Basic information

species Zea mays
transcript AC213600.3_FGT002
intron # 7
splice site 3'
intron type U2

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|211164201|gb|FL365727.1|FL365727
EST:     CGCAGGAGTCTGCAGCACCTACCATAGAGAAG                         GATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
genomic: CGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
EST: gi|211157759|gb|FL361265.1|FL361265
EST:     CGCAGGAGTCTGCAGCACCTACCATAGAGAAG                         GATTCTAGCCCTGACAATCCTGA
genomic: CGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGA
EST: gi|67033121|gb|CO461870.1|CO461870
EST:     GAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACTTACCATAGAGAAG                         GATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
genomic: GAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
EST: gi|60340820|gb|DN207793.1|DN207793
EST:     GAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAG                         GATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
genomic: GAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
EST: gi|32857890|gb|CD997571.1|CD997571
EST:     GAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAG                         GATTCTAGCCCTGGCAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT
genomic: GAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGT

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: 60

CATGGTTCTGTAAGCAAAGATGGTATTAGCGTTGAAGGTGGAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

CATGGTTCTGTAAGCAAAGATGGTATTAGCGTTGAAGGTGGAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

CATGGTTCTGTAAGCAAAGATGGTATTAGCGTTGAAGGTGGAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 57

CATGGTTCTGTAAGCAAAGATGGTATTAGCGTTGAAGGTGGAACTGTAGATGAATTGCCGCAGGAGTCTGCAGCACCTACCATAGAGAAGgttatatatt ... tgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggatgcaccatgccaccacagtttatgaagcatttgtcttggtgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG
                        tttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccccgcaggtcgagtttttttaataattcctattattattgttttggggatgcaccatgccaccacagtttatgaagcatttgtcttggtgaatttcagGATTCTAGCCCTGACAATCCTGAGGGTTTATCTAGGGAAGAGTTAGGTCGTATGGTGGCTTCTCGTTGGACTGGGGAAAGTGTAACTGAGGTTAGTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-ccccgca
- - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagca