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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 19
---gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
       |||||||| ||| |  |   |    |||| | | |||||| |||||| | || ||| | | || | ||| |    ||||  ||| || | || |||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||||
tattgtgttgttaatatagcattactctg---acttgaaagtgatgtagtgatgcttttcccatgattaacactctgagctatttggcatttttatgctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgat---ctttccaagttgaatattctaatgcttttgaaattctt-gttctt-cagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
     | | |     |||   | ||    ||||| || |  | |  ||||  |   ||||    | || |  |  |||       ||  || || ||| ||  |||||||||||||||| |||||||| ||||| |||| ||||||||||||| | || || ||  | || |||
----atatgagccctgtatcgt-ttccatacttactattctttttctgatcttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 19
---gtcattgttaatgtagtacaatgttatgcacttaat--aatga-tgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
    | ||| ||| | |  | ||   ||| |  ||||    ||||| || | |||  ||| |      ||    | | || ||    |   | | || || | |||||||||||||||||||||||||| ||||| |||| |||||| |||||| | || || ||  | || |||
ttttttatttttattttttt-catctttaggttcttatctcaatgaatgacttga--atcgtgtggcatttgtgaatttactgtgcct---actattattgtgcagGAAATTAAGTTTGAGCCAAATGTTATGTGTGAACCTATTGATAAGAAAGTAACATTTCGAGCAAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 19
---gtcattgttaatgtagtacaatgttatgcactta-ataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
   | | || ||  | |  | ||   |||    || |  | |    ||       ||| |      |||   | |  | ||    |   | | || || | |||||||||||||||||||||||||| ||||| ||||  ||||| |||||||| || || ||  | || |||
aaggaccttcttt-tatttttcatctttagtttctgatgtgaacgagtgacttgaatcgtgtggcattggtgaattaactgtgcct---actattattgtgcagGAAATTAAGTTTGAGCCAAATGTTATGTGTGAACCCATTGATAAGAAACTAACATTTCGAGCAAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 19
-------------------------------------------------------------------------------------gtcattgttaatgtagtacaatgttatgcacttaataatgatg--tcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
                                                                                          |||  |   |  ||||    ||| |  | |  || |||  ||   |  || ||  | ||||| ||  |   ||    |  |    ||     | |||||||| ||||||||||| ||||| |||||||| || ||||| |||||    ||||||    |||| |||
gtataatgactcagtagtttgatgaagtttgtaatttctcactctcttctggatgttctaaaacttgaccttctatttatttgaaaaaggtgtccacaaataacaacacaatgaatgtgaggattatgagtcagcactattttcgccagttggatcattctatctaatccatgcactaagcttgcagGAAATCAAGTTTGAGCCGAATGTCATGTGCGAGCACATTGAAAAGAAGTCCACTTTCAAGGCTAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 16
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgt-gatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
                                             || ||| || |||  |  ||  |||||    |||||     ||| || |||  ||||||||||| ||||| || ||||||||||||||||  ||||||||||||||||| || ||    ||||||
---------------------------------------------gtagataatgttttta--ttctatattgatttgcttc-atcattgtt-ttcgacagGAAATTAAATTTGACCCGAATGTGATGTGCGAACCAATTGACAAGAAACTTACGTTTCGAGACAGTCAG

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:     TGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTATATGAG                         GAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTT
genomic: TGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTATATGAGgtgcttcaca ... tgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTT




















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: 236

TAGGCTTTTTGTGAAGGCTCTGGGAAAACCGTCTGAAATATTGACAAAACTGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTATATGAGgtgcttcaca ... tgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

TAGGCTTTTTGTGAAGGCTCTGGGAAAACCGTCTGAAATATTGACAAAACTGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTATATGAGgtgcttcaca ... tgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

TAGGCTTTTTGTGAAGGCTCTGGGAAAACCGTCTGAAATATTGACAAAACTGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTATATGAGgtgcttcaca ... tgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

TAGGCTTTTTGTGAAGGCTCTGGGAAAACCGTCTGAAATATTGACAAAACTGAATGAAATGGCTGGATTTTCTCCAAATGAAGAAATTGAGCTATATGAGgtgcttcaca ... tgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
                        ttctaat  putative branch site (score: 196)
                                         ttcttgttcttc  putative PPT
                 ttgaatattctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - tatgcac
- - - - - - - - - - - - - - - - - - -atgatgt
- - - - - - - - - - - - - - - - - - - - - - -gtgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctt