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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgccttgatttctctattttttttatgttcactgcttacatgatctatcatatacttccaagtgtgatttgtatgttgcatgctcttgatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG

Basic information

species Zea mays
transcript GRMZM2G347541_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
gttggtgccttgatttctctat-tttttttatgttcactgcttacatgatctat-catatacttccaagtgtgatttgtatgttgcatgctcttgatgttcact--------ttatttcggcct-tagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG
|||||||| || |||||  ||  ||| | | ||||  ||  || ||||||  |    |||||  | |||  | | |||  ||   | |||| ||  | ||   |        ||| ||||   | |||||||||||||||| |||||| | |||||||||||||||||||||||||| |||||||| |||||| |||||||||||
gttggtgcattaatttcaataggtttctatctgtttgctcatt-catgataaaaatttatacagc-aagcttaacttgcttgggccttgcttttagtatttgttcattcatgttacttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
gttggtgccttgatttctctat-tttttttatgttcactgcttacatgatctat-catatacttccaagtgtgatttgtatgttgcatgctcttgatgttcact---------------ttatttcggcct-tagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG
|||||||| || |||||  ||  ||||| | ||||  ||  || ||||||  |    |||||  | |||  | | |||  ||   | |||| ||  | ||   |               ||| ||||  || |||||||||||||||| |||||| | |||||||||||||||||||||||||| |||||||| |||||| |||||||||||
gttggtgcattaatttcaatagatttttatctgtttgctcatt-catgataaaaatttatacagc-aagcttaacttgcttgggccttgcttttagtatttgttcattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
gttggtgccttgatttctctattttttttatgttcactgcttacatgatctatcatatacttccaagtgtgatttgtatgttgcatgctcttgatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG
    |   ||     ||| |    |    ||||  | ||  | | | ||||  | |    ||  |     || ||| || |    | |  ||||| |   ||||           ||| ||  ||||||| |||||| |  | ||||||||||| |||||||| || || ||||| ||||| |||||||||| |
-caagcaactca---tctttcacctggcaatgtgtaatg--tgcgttatcttcccttattttggataaaagaattg-atatcaggtaccattgat-tattctttgc---------agACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------gttggtgccttgatt------tctctattttttttatgttcact---gct-tacatgatctatcatatacttccaagtgtgatttgtatgttgcatgctctt--gatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG
                                                   | |  ||||||       | | ||||||    |  | || |   ||| | | | ||   | || || |      | | ||  |   |  | ||  | ||  ||  | |   | ||||  ||   |||| |  |||| || || ||  | || ||||| ||||| || |||||||| || ||||||||||| |||||||||| |
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgc---agATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG

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|71299569|gb|DR785796.1|DR785796
EST:     TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|67021468|gb|CO450217.1|CO450217
EST:     CTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: CTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211315827|gb|FK969310.1|FK969310
EST:     TGYSSTGGNCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGG
genomic: TGTGCTGG-CTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGG
EST: gi|67028179|gb|CO456928.1|CO456928
EST:     TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211315829|gb|FK969312.1|FK969312
EST:     TGTS-TGGNCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGGT--CTGTTGGCAAGATA
genomic: TGTGCTGG-CTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211315828|gb|FK969311.1|FK969311
EST:     TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTARAGAACAATGGTGGCTGTTGGCAAGATA
genomic: TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211301945|gb|FL333154.1|FL333154
EST:     CCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
genomic: CCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATA
EST: gi|211313818|gb|FK969308.1|FK969308
EST:     TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATG                         ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTG
genomic: TTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTG

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: 333

GGAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

GGAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

GGAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 177

GGAAGCTTGACAAAGGAGCAGTTCTTAAAGCACTTTGTGCTGGCTTTAGGGAAACCACCGAGCCAGCCGTTTGCTTGAGTGATGgttggtgcct ... tcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagtgtgatttgtatgttgcatgctcttgatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG
                          tcttgat  putative branch site (score: 177)
                                      ctttatttc  putative PPT
                                     actttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgccttgatttctctattttttttatgttcactgcttacatgatctatcatatacttccaagtgtgatttgtatgttgcatgctcttgatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA