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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactggcgttattactctactttttgctggtatcaacagttacttacacgagaattttttttttctcgtaacttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA

Basic information

species Zea mays
transcript GRMZM2G086052_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g40620.2 (Oryza sativa), 3'ss of exon 9
gtatgcactggcgttattactctactttttgctggtatcaacagttacttacacgagaatttttt-------ttttctcgtaacttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA
|| ||||| |   |  | | ||  |||| |||| || |      |     | || |  |||| ||        | ||| | |  ||  ||||| ||||| || || |||||||||||||| || ||||||||| |||| ||||| || || |||||| | || ||||| || || || |||||  |    ||
gtttgcacagatatcttaaatc--ctttctgcttgtttttctcat-gtccagacaaacatttcttactaggtctgtcttgaactttctgcagATGATATTTCTGTTCATGGGCCAATGACTCAATCCCAGTTCTTGGGCTCTCTTGGTATAAACTTCCGTGTGGAAGCCCTGCTCCAAAACTGTGCTACTGA

upper sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT3G28700.1 (Arabidopsis thaliana), 3'ss of exon 9
-------gtatgcactggcgttattactctactttttgctggtatcaacag-ttacttacacgagaattttttttttctcgtaacttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA
          |  ||||||  || || ||    |  ||  ||||     || ||||||||  || ||      | |    ||   ||  |||||  || |||| |||||||| || ||||| |||||||||||| ||||||| || || || |||||||| || || ||  | || ||||| || | ||| ||
gtttcgttcctatactggc--tactagtcattgtgatgtaggtagggttagcttacttacttgacaaagcaaatgt----gtgtgttctgcagAAAATGTCTCAGTCCATGGACCTATGACTCAGTCCCAGTTCTTGGGTTCGCTTGGAATAAACTTCAGAGTTGATGCATTGCTACAGAATTGTAACGACGA
















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|91048588|gb|EB159006.1|EB159006
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|76924986|gb|DV170229.1|DV170229
EST:     CCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: CCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|60359085|gb|DN226058.1|DN226058
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|211258233|gb|FL463465.1|FL463465
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|76015304|gb|DT942474.1|DT942474
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|71313521|gb|DR793328.1|DR793328
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|71772607|gb|DR970535.1|DR970535
EST:     GCCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAAGGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: G-CCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|71326242|gb|DR799815.1|DR799815
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|78108017|gb|DV526435.1|DV526435
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|78090508|gb|DV518882.1|DV518882
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|74243641|gb|DT651555.1|DT651555
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
EST: gi|71297895|gb|DR784918.1|DR784918
EST:     TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAG                         ACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC
genomic: TGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTC

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: 104

AAACACAAGTTTGTGGACATATTAGACGATCCTGGCTCCGCTGATTTGAGTGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 27

AAACACAAGTTTGTGGACATATTAGACGATCCTGGCTCCGCTGATTTGAGTGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 58

AAACACAAGTTTGTGGACATATTAGACGATCCTGGCTCCGCTGATTTGAGTGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA


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

AAACACAAGTTTGTGGACATATTAGACGATCCTGGCTCCGCTGATTTGAGTGCCTACGTTGATTTTGCTTCGATCAAGCGCTCCGCCGAGGAAGCTTCAGgtatgcactg ... acttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctggtatcaacagttacttacacgagaattttttttttctcgtaacttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA
                         agaattttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcactggcgttattactctactttttgctggtatcaacagttacttacacgagaattttttttttctcgtaacttgcgcagACGATATCTCGGTCCATGGGCCAATGACGCAGTCCCAGTTCCTGGGTTCTCTCGGCATCAACTTCAGGGTAGAAGCTCTCCTGCAGAACTGCACCGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG