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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgccactgtacctattcatatgtttccttgaatgtgattgtctcaactttaattgctatatgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 8
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 8
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 3'ss of exon 8
gcatgccactgtacctattcata--------tgtttccttgaatg---------tgattgtctcaactttaattgctatatgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA
||||||||||| |   ||  |||        || |  || |||           ||||| ||||||   |  |  ||||||  ||||||||||||||||| |||||||||||||||||||| ||||| |  ||  | || ||||| || ||||||||||| |||||||||||||||||||||||||| |
gcatgccactgaaagcatatatacttcttggtgctctctagaacactgaacatttgattatctcaaacatcttgactatatttttgcagTGGAGTCCCACAGAAGCCGACATATTTGCCTCTTGTTCAGCCGACAGAACAATATCTATCTGGGATATACGGACAGGGAAGAAACCTTGTATTTCTGTTA

upper sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g03822.1 (Oryza sativa), 3'ss of exon 8
gcatgccactgtacctattcata--------tgtttcct-------tgaatgt--gattgtctcaactttaattgctatatgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA
||||||||||| |   ||  |||        || |  ||       |||| ||  |||| ||||||   |  |  ||||||  ||||||||||||||||| |||||||||||||||||||| ||||| |  ||  | || ||||| || ||||||||||| |||||||||||||||||||||||||| |
gcatgccactgaaagcatatatacttcttggtgctctctagagcactgaacgtttgattatctcaaacatcttgactatatttttgcagTGGAGTCCCACAGAAGCCGACATATTTGCCTCTTGTTCAGCCGACAGAACAATATCTATCTGGGATATACGGACAGGGAAGAAACCTTGTATTTCTGTTA
















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|32866681|gb|CF006363.1|CF006363
EST:     TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAG                         TGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
genomic: TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
EST: gi|211517252|gb|FL335507.1|FL335507
EST:     TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAG                         TGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
genomic: TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
EST: gi|211303562|gb|FL306499.1|FL306499
EST:     CCCA-TTGTTGGACACTCTGCAAGTGTTGAAGATCTACAG                         TGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
genomic: CCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
EST: gi|31349324|gb|CD433681.1|CD433681
EST:     TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAG                         TGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
genomic: TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
EST: gi|31350283|gb|CD434640.1|CD434640
EST:     TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAG                         TGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG
genomic: TAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACG

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: 47 (upstream exon), 49 (downstream exon)
Score: 199

CTGCAATAAGTGCATTCACCTATGGGAGCCGACTTCAAACAACTGGAACGTAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

CTGCAATAAGTGCATTCACCTATGGGAGCCGACTTCAAACAACTGGAACGTAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 137

CTGCAATAAGTGCATTCACCTATGGGAGCCGACTTCAAACAACTGGAACGTAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 122

CTGCAATAAGTGCATTCACCTATGGGAGCCGACTTCAAACAACTGGAACGTAGATGCAAACCCATTTGTTGGACACTCTGCAAGTGTTGAAGATCTACAGgcatgccact ... atgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatatgtttccttgaatgtgattgtctcaactttaattgctatatgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA
                                ctttaat  putative branch site (score: 122)
                                 tttaattgctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgccactgtacctattcatatgtttccttgaatgtgattgtctcaactttaattgctatatgcttgcagTGGAGTCCCACGGAAGCCGACATATTTGCCTCATGTTCTGTGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA