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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgttattgttgtacttttagtgcaatgcaaaaaatagtctacttatgccttacaccctttcccactcacttttctccccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA

Basic information

species Zea mays
transcript GRMZM2G163658_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 11
gtatcttgttattgttgtacttttagtgcaatgcaaaaaatagtctacttatgccttacaccctttcccac-tcacttttctccccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA--------------
  |   ||| ||   || |   |    || || |      ||  ||  ||     |    |     |  || | ||| || | ||  |||||| ||| |   | |||||||||  | | || || | || |||||| |  ||||||| |  |||| ||||||||||||||| |||||||||||| ||||  |               
--aaaatgtcataaatgcaaactgttggctatccc-----tatcctttttgcctgtagtgcttcccctaaccttactatttttcctctttaagcatgccgtcgccagCAGCTGACAGTCTGCAAAAGTTCTATTTGGATTTGAGAAAACAAAGTGATTCTGCTGATGGTACGCCCATCACAGCCCGGCAACTGGAAAGCCTTGTAAG
















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|32857873|gb|CD997554.1|CD997554
EST:     CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAG                         AATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
genomic: CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
EST: gi|32942785|gb|CF047604.1|CF047604
EST:     CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAG                         AATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
genomic: CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
EST: gi|60354226|gb|DN221199.1|DN221199
EST:     CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAG                         AATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
genomic: CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
EST: gi|88752654|gb|DY536795.1|DY536795
EST:     CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAG                         AATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
genomic: CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
EST: gi|32857853|gb|CD997534.1|CD997534
EST:     CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAG                         AATGGCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
genomic: CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
EST: gi|32942784|gb|CF047603.1|CF047603
EST:     CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAG                         AATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG
genomic: CAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAG

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: 111

GGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATTATCTGGGCAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATTATCTGGGCAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

GGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATTATCTGGGCAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

GGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATTATCTGGGCAACTTCTTCGCAAATATATATCTTATTCAAGAGAACATGTCTTCCCCAGgtatcttgtt ... cccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatagtctacttatgccttacaccctttcccactcacttttctccccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA
                               cactcac  putative branch site (score: 16)
              tgccttacaccctttc  CT-rich tract
                                                ttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttgttattgttgtacttttagtgcaatgcaaaaaatagtctacttatgccttacaccctttcccactcacttttctccccttttaagAATGTCAAAGGCAGCAGCTGCAATTTTGAAAGAATTTTATTTGAAGCTGAGAAACCGCAGTGCTTCTGCTGATGGTACACCCATCACAGCCAGGCAGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT