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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacattctaatttgcattagaaaagtttacaatatggttactgtttcttccttttctctgacagtagatgtactttaaaagattgttttttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 13
catacattctaatttgcattagaaaagtttacaatatggttact-gtttcttccttttctctgacagtagatgtactttaaaagattgttttttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG
 |     | | |   ||   |      ||   |  ||  | | | || ||  |   || | | |  |   |  |   |||| || |  || |||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||||| || |||||||| |||||| | || |||
-acctccttttaacagctgcactgtgcttcggataattttaaatagtgtcccctgattgtataagggcctacttttcttaagagttctttctttgttgcagATCAAGGACGAAGTTAAGGCTGTTTTGGACTTCATCAATTATGTTTACGAGATATTTGGATTTAAATATGAATTGGAGCTATCAACG

upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 12
catacattctaatttgcattagaaaagtttacaatatgg-ttactgtttcttccttttctctgacagtagatgtactttaaaagattgttttttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG
          | |||   ||  |||  | | ||| ||   |   ||     || |||   ||||   | || ||  ||    |  ||| ||| | || ||||| ||||||||||| | |      ||| | |||||||||||||| ||| |||||||||| |||| ||||||| || || | || |||
-------gtgagtttatcttt-aaatttctgcaacataaatctttgaagtctcttttgagctgaattttga-gtgatt----aatttgatttattttacagATAAAGGATGAAGTGAGGAACAGCTTGAATTTCATCAATTATGTCTATAAGATATTTGGTTTCACATATGAGCTGAAGCTTTCAACG
















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|211046688|gb|FL336954.1|FL336954
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|32832908|gb|CD972586.1|CD972586
EST:     CAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: CAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|67033102|gb|CO461851.1|CO461851
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|22545540|gb|BU097899.1|BU097899
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|211403724|gb|FL311348.1|FL311348
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|211181488|gb|FL345837.1|FL345837
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|32934180|gb|CF038992.1|CF038992
EST:     CTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: CTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|32832310|gb|CD971988.1|CD971988
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|211197538|gb|FL314132.1|FL314132
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTNAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|32834031|gb|CD973709.1|CD973709
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|50324858|gb|CO519984.1|CO519984
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
EST: gi|20802797|gb|BQ293847.1|BQ293847
EST:     GATGATGCTCATATCTTCTGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATTGA
genomic: GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTAT-GA
EST: gi|32835314|gb|CD974992.1|CD974992
EST:     TGCAGAGAAGACCAA                         ATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG
genomic: TGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAG

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: 42 (upstream exon), 49 (downstream exon)
Score: 433

GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 232

GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 273

GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 162

GATGATGCTCATATCTTCTGCAGAGAAGACCAAgtaggtttta ... tttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttccttttctctgacagtagatgtactttaaaagattgttttttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG
            ctctgac  putative branch site (score: 162)
                                       ttgtttttt  putative PPT
                           tactttaaaagattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacattctaatttgcattagaaaagtttacaatatggttactgtttcttccttttctctgacagtagatgtactttaaaagattgttttttgttgcagATCAAGGATGAAGTTAAGGCTGTTTTGGAATTCATCAATTATGTTTATGAGATATTTGGCTTCAAATATGAGTTGGAGTTGTCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
catacat
- - - - - - -ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgtac