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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgttatgattaggtcagctggatttttaatgtagttattctaactataagattaataatgctgttactgaatgtgcttttttaatccttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG

Basic information

species Zea mays
transcript GRMZM2G080044_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080044_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g11140.1 (Oryza sativa), 3'ss of exon 2
gtttgttatgattaggtcagctggatttttaatgtagttattct--aactataagatta--ataatgctgttactgaatgtgcttttttaatccttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG
  |   | |     |   || | |||||  |  ||  |||| ||  ||| |  | |||   |||||  | ||||||||| |||  | ||   |||||||||||| | |||||||||||||| || |||||||| ||||||||||||||||| ||| | ||| | ||||||||||| |||||||||||||||| |||||||
-ataaatgtttgaggaaaagttagatttacagcgtgcttatgctataaccactatatttgtataattgtattactgaatatgccctctt---ccttattttcagCGTCCACGAGTGTGCATCTTGGGTGGTGGATTTGGTGGCCTGTACACTGCTCTTAGATTAGAATCTCTTGTATGGCCCAATGATAAGAAGCCTCAG

upper sequence: GRMZM2G080044_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G08740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgttatgattaggtcagctggatttttaatgtagttattctaactataagattaataatgctgttactgaatgtgcttttttaatccttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG
||| || ||  |      ||   ||| | | |  |||       ||   |   |||  | || | || ||| |||     | | |  ||  | ||| ||||| ||| | ||||||||| |||||||||| ||||| ||  ||||||| ||||| ||| | ||||||||||| |||||  | || || | |||||||
gttcgtaattctc----tagaacgatgtatgagataga------aaaagttcaattgctgatcccgtaacttaat-catgtatatgctctctctttacagAGGCCAAGGGTGTGCATTCTAGGTGGTGGCTTTGGAGGATTGTACACAGCTTTGAGATTAGAATCTCTTGTTTGGCCTGAAGACAAAAAGCCTCAG
















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|30306789|gb|CD001462.1|CD001462
EST:     TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAG                         AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
genomic: TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
EST: gi|29543792|gb|CB604172.1|CB604172
EST:     TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAG                         AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
genomic: TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
EST: gi|211318167|gb|FL216125.1|FL216125
EST:     CTGACGAAGCAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAG                         AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
genomic: CTGACGAAGCAGCA-C-C-ATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
EST: gi|31998276|gb|CD662009.1|CD662009
EST:     TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAG                         AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
genomic: TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
EST: gi|211318171|gb|FL216129.1|FL216129
EST:     CTGACGAAGCAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAG                         AGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTATACCGCT
genomic: CTGACGAAGCAGCA-C-C-ATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCT
EST: gi|211318168|gb|FL216126.1|FL216126
EST:     TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAG                         AGACCACGAGTGTGCATTTTAG-TGGTGGGGGTTTGGTGGCCTGTACACCG
genomic: TGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGG--TTTGGTGGCCTGTACACCG

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: 48 (upstream exon), 43 (downstream exon)
Score: 22

GTGCATGGCTTCAAGTGGCTCTGGTGATGGTGATTTTGCTCGGTCTACATTGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

GTGCATGGCTTCAAGTGGCTCTGGTGATGGTGATTTTGCTCGGTCTACATTGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG


Block sizes: 44 (upstream exon), 21 (downstream exon)
Score: 3

GTGCATGGCTTCAAGTGGCTCTGGTGATGGTGATTTTGCTCGGTCTACATTGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 12

GTGCATGGCTTCAAGTGGCTCTGGTGATGGTGATTTTGCTCGGTCTACATTGACTGACGAAGCAGCACCATTTCCATTATACTCTTGGCCAGATAAGCAGgtcgactgat ... ttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actataagattaataatgctgttactgaatgtgcttttttaatccttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG
                                 cttttttaatcctt  CT-rich tract
                                  ttttttaatccttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttatgattaggtcagctggatttttaatgtagttattctaactataagattaataatgctgttactgaatgtgcttttttaatccttattttcagAGACCACGAGTGTGCATTTTAGGTGGTGGGTTTGGTGGCCTGTACACCGCTTTAAGACTTGAATCTCTTGTGTGGCCCAATGATAAGAGGCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - tcagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg