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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaactttatttgtaaaaaatgaaaatag

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 14
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctgg------tcttgtttcagtcataccagcagctaactctcttggtga-ctcctcttgatagaactttatttgtaaaaaatgaaaatag
||||||||||||||||||||||||||||| || |||||||||||||| ||  ||||||||||||||||||| |||||||||||||||       | ||||| |||  ||   |    ||| |||| | |||| ||  | || |||      |   | |    ||||    |||
ATAAGGTTGAAGAAAGAACAAGAAGAGAAGGAACACAAGAAGAAGGAAAAAGCTGAAGCTCATCTCTACACCATCATAAAGgtctggataagaacctgttttagttttaatggt--ttaaatctcattgtgaacttttttttataa-----tggctatgtgcaatgtccctag

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 10
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtc-tggtcttgtttcagtcataccagcagctaactctcttg-gtgactcctcttgatagaactttatttgtaaaaaatgaaaatag-----------------------
|| || || |||||||||||||| || |||||||  |||| |||||||||| |||| |||||  | ||||| | |||||||||  |     | | |   |  |||    | |    |   |||  |||      |    | || || ||  ||  | | | || ||                         
ATGAGATTAAAGAAAGAACAAGACGAAAAAGAGCTGAAGAGGAAGGAGAAGGCTGAGGCTCACTTGTACACCACCATAAAGgttgtaactctatctttcttttactttgacccctttactttgtatgatattggtatgcataa-ttgataagttgagattcaatattatgttattgattcattggtcccag

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 14
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgt--ctggt---cttgtttcagtcataccagcagctaactctcttggtgactcctcttgataga-actttat-ttgtaaaaaatgaaaatag--------------------
   |||||||||||||| |||||||| ||||||||||| || || || ||  | || ||||| || |||||||| ||||||||  || ||   || ||| |   | | | | |    || |   |   |     |  |  |||||  || |   |||   || |  ||| |                      
GAGAGGTTGAAGAAAGAGCAAGAAGAAAAAGAGCACAAAAAAAAAGAAAAAGCAGAGGCTCACCTTTACACTATTATAAAGgttcctagttggctagttcctaacttgctatcctagaattgagtactttgtgtccttacatagatgctgtgggttgcttaataccaaactgttaacatgtgatacttcttag

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 14
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaacttta-tttgtaaaaaatgaaaatag-------------------------------
||||||||||||||||||||||||||||| ||| | ||||  ||  | ||  |  |||| || || |  ||||| ||||||||   ||| ||||||  || | ||  ||      | |  |||| |    ||| || |  |||  |   |||     |||   ||                                 
ATAAGGTTGAAGAAAGAACAAGAAGAGAAGGAGGATAAGAGAAAATATAAAGCACAAGCCCACCTTTTTACTATTATAAAGgta-agtcgtgtttctttcttgccctca----ttttttgtggtaataggtctagaaatgactggaacctgttgctcatggggatcttttaactaaaataatcaatcgatgcatctag

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 14
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaactt---tatttgtaaaaaatgaaaatag
||||||||||||||||| || || ||||| || |  |||| |||||| ||| |||| || || || |||||||||||||||||      ||   |   |  |   |     |   | |   |  | |    ||| | || | ||   |||| ||  |   |    ||||
ATAAGGTTGAAGAAAGAGCAGGAGGAGAAGGAACGGAAGAGGAAGGAAAAGGCTGAGGCCCACCTTTACACTATCATAAAGgtaaacaattaactgtatggt-ttattttttggttgtag-gaagccgtagcttcagagtaattaattattcgtttacgttatgtatag

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ18164 (Selaginella moellendorffii), 5'ss of exon 12
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtcttgtt-tcagtcataccag-cagctaactctcttggtgactcctcttgatagaactttatttgtaaaaaatgaaaatag
 | ||| | ||    ||  | || || |||||| | ||   ||| |||||||||||||||||| | |||||| ||||||||||         || ||  | ||    | | | | || || ||                                             
GTGAGGCTAAAACGGGAGTACGATGACAAAGAGAAAAAACGGAAAGAGAAGTCTGAAGCTCATTTGTACACTGTCATAAAGGTAgtccaccattgtctttgattttggtctgttgacgcttttaccag----------------------------------------

upper sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 12
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaactttatttgtaaaaaatgaaaatag
 | ||| | ||    ||  | || || |||||| | ||   ||| |||||||||||||||||| | |||||| ||||||||||   |||   | |      |  |      |   |||||||  |  |   |  |                               
GTGAGGCTAAAACGGGAGTACGATGACAAAGAGAAAAAACGGAAAGAGAAGTCTGAAGCTCATTTGTACACTGTCATAAAGGT--Agtccactattgtctttgtc-----tttggtctcttgacgcttttaccag-------------------------------

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|211312723|gb|FL362682.1|FL362682
EST:     AGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAG                         ATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTT
genomic: AGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtctt ... atgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTT




















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), 46 (downstream exon)
Score: 431

ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtctt ... atgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 487

ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtctt ... atgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 435

ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtctt ... atgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 403

ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtctt ... atgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGGTTGAAGAAAGAACAAGAAGAGAAAGAGCACAAGAAGAAGGAGAAGTCTGAAGCTCATCTCTACACTATCATAAAGgtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaactttatttgtaaaaaatgaaaatag

- - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA