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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA

Basic information

species Zea mays
transcript GRMZM2G458208_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 3
------gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
      |   |   ||    ||  | |  || ||||  |||| | |||   ||| ||||    | |  ||||        ||| | |||  |  |   || ||||||| |||||||||||||||||||| |||| |||| ||||||||||||||||||| ||||||||||| || ||||||||||| || ||||||||||| ||||
agcacagtgtttgttgggcctacaacttttt-atgt-ttttattttgtcagagtgctgtgttgtgttatttgca----gattggacttaacgtgtctattatgcagGGACGCAATGTGGTTATTGAGCAGAGCTATGGTTCACCGAAAGTCACAAAGGACGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------gcactcactgattataatattgctt---gatgt--gctttac---tctgttgtagtactgttgcatttagtttgttttgtacttgaatttattg-----cctgc-tttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
                                                                          |   ||   |  || |  ||  |||   ||| |  | || |    ||  |  |||| | |     ||||||| || |||  |  || | | |||     | ||  ||| |  ||||||| |||||||||||||||||||| ||||| ||||| ||||| || || ||||| || || || || |||||||||||||| ||||| | ||| ||||
gtaaccaagcttatgcctgatagtttcttggcaaaagttgtacctgtgtttttattcaatcatttatttattcggttttctaagggtagagcatgtcttttggatctaggattgatatttcaatcctagtcccggcat-tttagttggtgttgatcacgattgttttgttaaacttgtgtttttttagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCTAAAGTGACGAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
-gcactcactgattataatattgc-ttgatgtgctt-tactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
  || |||  |||  ||||  ||   || || | || |    ||   | || |  | |  | | || ||| |||   |    || | |   | || | |  ||||||| ||||| || ||||||||||| |||||||| || ||||| || || ||||| || ||||| ||||||||||||||||| ||||||| ||| ||||
aacagtcaaagatgttaatgctggactgttgagtttgtgtattgccattgtgcaatag-gtgttgtctgtgttg-gttgatgttgagtttattctcttt-tagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 3
gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaat-ttattgcctgctt------tctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
           ||  |     ||||||      | |     | ||||| |  |    |||  || || |||  |  || | ||||||     ||      | |  ||||||| |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| || || || || |||||||||||||| ||||||| ||| ||||
--gaatgtcttttggatccaggcttgaaacatatca----atagtagtcccttcat-tttgattggtgttgatcacgattgttattgttaaattggtgtttttatagGGGCGTAATGTGGTTATTGAGCAAAGTTTTGGAGCACCCAAAGTGACAAAAGATGGAGTAACCGTTGCTAAGAGCATTGAATTCAAGGATAAAGTCAAGA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 3
------gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
        | | |  |||  ||||  ||     | ||  |    |  ||||   |  | ||   |  || | | |||   |||| ||||||  ||  |      |||| || ||||| || ||||||||||| |||||||| || ||||| || || ||||| || ||||| ||||||||||||||||| ||||||| ||| ||||
aacaaaagaatgaacgatgttaatgctggactttttgtgtattgccattgtgcaatgggtgttgtctgtgtttgttgatgttgagtttattatctttt------agGGCCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------gcactcactgattataatattgcttgatgtgct-ttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgc---------tttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
                                                    | |   | | |  |  | ||  | ||| |  || ||     ||   |  | |  |   ||| |||    |   |||      || | | ||          ||| || |||| || |||||  | || || |||||||  |||||||| || || |||||||||||||||||||| || ||||||||||| || ||||||||| | ||||
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA

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|31355867|gb|CD440224.1|CD440224
EST:     GGGGTGTTGAGGAGTTGGCAGATGCCGTCAAAGTGACAATGGGACCTAAG                         GGCCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|61119163|gb|DN560124.1|DN560124
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGCCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCCAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|89754394|gb|DY685176.1|DY685176
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|88747169|gb|DY531310.1|DY531310
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|31441079|gb|CD510510.1|CD510510
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|31349389|gb|CD433746.1|CD433746
EST:     GGGGTGTTGAGGAGTTGGCAGATGCCGTCAAAGTGACAATGGGACCTAAG                         GGCCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|94476466|gb|EB705424.1|EB705424
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|26557261|gb|CA829496.1|CA829496
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|31355665|gb|CD440022.1|CD440022
EST:     GGGGTGTTGAGGAGTTGGCAGATGCCGTCAAAGTGACAATGGGACCTAAG                         GGCCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
EST: gi|8367181|gb|BE050126.1|BE050126
EST:     GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAG                         GGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG
genomic: GGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAG

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), 49 (downstream exon)
Score: 309

TGCTGCGAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 161

TGCTGCGAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 152

TGCTGCGAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 190

TGCTGCGAAGGACATCAAGTTTGGTGTTGAGGCCCGTGCTCTGATGTTGAGGGGTGTTGAGGAGTTGGCAGATGCTGTCAAAGTGACAATGGGACCTAAGgtataaccac ... ctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
                                         cctgctttct  CT-rich tract
           atttagtttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcactcactgattataatattgcttgatgtgctttactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - actgatt
- - - - - - - - - - tgcttga
- - - - - - - - - - - - - -tgtgctt
- - - - - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcctg