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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttattacaagaactaatagcacactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG

Basic information

species Zea mays
transcript GRMZM2G356938_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g57240.1 (Oryza sativa), 3'ss of exon 1
aacactatttgcccatgaatagttttaaaaa-----aagtcaaacagatcaccctgtgcatgtagtttttattacaagaactaatagcacactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
  || |   |       | |  |||| || |     | | |||| || | |     ||  |||| || |  | ||||||| |||    |   ||   |||||||||| || |||||||| || || ||||||||||| |||||| | || |||||||||||||| ||||||||||| ||||| || |||||||| ||| ||||||
-ccaatgcattgtagcaagtccttttgaagattaagatggcaaaaagtttattgc-tgtgtgtaattgt-gtaacaagaagtaacg--atcttgtacttctgcagGTGGAATCTGAGTTCTTACCTCTTTACAGCACGTATGGCCTGGGTTTGACTACATGGAGCCCTCTAGCTTCGGGAGTTCTCACTGGAAAGTATGCCAAAG

upper sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G19000.1 (Glycine max), 3'ss of exon 1
aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttatt--acaagaactaatagcacactgctt--ttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
   ||  ||      ||  ||  ||  |      |        | |   ||    || |||||| |    |   ||  |  ||    |||   |  |  |||||||||||||||||||| | || || |||| || ||||||||  ||  | ||||||||||||||||| || || ||||| || ||||| |||||||  ||||
--tacatttatgttttgtgta--ttccatgcctttttttttttttaatttggttttggagttttcacctgattggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG

upper sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G24620.1 (Glycine max), 3'ss of exon 1
aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttattacaagaactaatagc---acactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
|  |||        |||  | ||   |   || |||       | |    ||     |  |||    ||   |  ||  |      ||       |  ||||||||||||| |||||| | || || |||| || ||||||||  ||  | ||||||||||||||||| || || ||||| || ||||| |||||||  ||||
agaactg--catttatgttttgtgc-atttaatgtctcttcttttatttggttttgatgttttcacctaattgggcttttgatttgacttgatcatgttgcagGTTGAGTCGGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG

upper sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ28469 (Selaginella moellendorffii), 3'ss of exon 1
--aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttattacaagaactaatagcacactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
   | |   |    | |  | | || |   |     |        |  |   |    |      || |||||     | |         | ||||  | ||||| ||    || | | | ||||| ||||| | |||||| |||||  |||| || ||||||||||| || |||||||| || |||||||| ||||||||| 
gtgaaagattccagctac-agtggtgtgtcactctttttcgttctttgcttggaattttggtcattgattacgctctccatctttgt-tttctttcttccagGTGGAAGTGGAATATCTTCCACTGTACAGTAGCTATGGGATCGGCGTGACGACTTGGAGTCCTCTGGCGTCAGGAGTTCTGACTGGAAAGTATACCAAAT

upper sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30357 (Selaginella moellendorffii), 3'ss of exon 1
-aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagttttt-attacaagaactaatagcacactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
  | |   |    | |  | | || |   |     |        |  |   |    |   ||  || ||||      | |         | ||||  | ||||| ||    || | | | ||||| ||||| | |||||| |||||  |||| || ||||||||||| || |||||||| || |||||||| || |||||| 
tgaaagattccagctac-agtggtgtgtcactctttatcgttctttgcttggaattttgggtcattgattatgctctccatctttgt-tttctttcttccagGTGGAAGTGGAATATCTTCCACTGTACAGTAGCTATGGGATCGGCGTGACGACTTGGAGTCCTCTGGCGTCAGGAGTTCTGACTGGAAAGTACACCAAAT

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|76287149|gb|DV026717.1|DV026717
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACGGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|71428195|gb|DR809245.1|DR809245
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|78084452|gb|DV512845.1|DV512845
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|76019266|gb|DT946436.1|DT946436
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTTGCCACTTTACAGCACCTATGGCATCGGATTTGA
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTT-GCCACTTTACAGCACCTATGGCATCGGATT-GA
EST: gi|148942706|gb|EC887730.2|EC887730
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|211498539|gb|FL364230.1|FL364230
EST:     TCGGACCCATCGTCGAGCAGCCGGAGTACAACCTTTTCTCCAGACGCAAG                         GKTGAGTCTGAGTTCTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|149015428|gb|EE045282.2|EE045282
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|13150478|gb|BG320800.1|BG320800
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTTTTCTCCAGACACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
EST: gi|149086227|gb|EE175767.2|EE175767
EST:     TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAG                         GTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT
genomic: TGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACT

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), 46 (downstream exon)
Score: 29

CGCGCAGCAGATCACCGAGGCCTGGGCAGTCGCCAACCGCCTCGACCTCGTGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 43

CGCGCAGCAGATCACCGAGGCCTGGGCAGTCGCCAACCGCCTCGACCTCGTGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 18

CGCGCAGCAGATCACCGAGGCCTGGGCAGTCGCCAACCGCCTCGACCTCGTGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 45

CGCGCAGCAGATCACCGAGGCCTGGGCAGTCGCCAACCGCCTCGACCTCGTGGGACCCATCGTCGAGCAGCCGGAGTACAACCTCTTCTCCAGGCACAAGgtgagctcgg ... ttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctgtgcatgtagtttttattacaagaactaatagcacactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG
                            aactaat  putative branch site (score: 45)
                                         ctgcttttct  putative PPT
               tttttattacaagaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttattacaagaactaatagcacactgcttttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
aacacta
- - - - - - ccatgaa
- - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acactgc