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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttagaccagtggtgttctttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 1
gtattttagaccagtggtgttctttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG
||||||||    |  | ||| |  | | ||     ||| | ||  | |||| |||||||||||  |||         ||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||
gtattttaactgaaagatgtaccctctttc-----ctgctatgaaccttcaactgatatttctcctat---------attgaagTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G19110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattttagaccagtggtgttc---tttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG
   | ||  ||      ||||    |  || |  || |||  |||  | | |  |    |||| ||  | ||    |  ||||  ||||  |  || | ||||||||||| |||||||||||| | || || || ||| |||||||||||||  |||||||  |  | || ||||||
--gtattgaactgcctttgtttaaatgcttttttttttcttgtttactgtatgtgtacttattcctcct-tttccctcctatt--agTCGCTCAGGAGAATGAATCATCCAAACATTGTGAAGTTGAAGGAAGTAATCCGGGAAAATGATATCCTATACTTTGTCTTTGAGTACATG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattttagaccagtgg-tgttctttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG
||| | ||   || | | ||     |||    || | | |||| | || |  | |     |  |||| || || | | |||  ||||  |  |  | ||||||||||| |||||||||||||| || || || ||| |||||||||||||  |||||||  |  | || ||||||
gtactgtatctcattagctgaaaggttttgtttttttttttttttactgtatgtt--cgctgatttttttcttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------gtattttagaccagtggtgttcttttta-----tcattctctgttttgt-------tctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG
                                          | ||  |    | ||| |||||| |      |    |  |  |||||       |  | ||  || ||   |    |||||  |||||    |||||||||||    |||||||||||||||| |||||||| || ||||||||| | ||||| |||  | | |  ||| |  | || || |||
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggtttta--acagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG

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|211443458|gb|FL042456.1|FL042456
EST:     AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|211443465|gb|FL042463.1|FL042463
EST:     AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|60345317|gb|DN212290.1|DN212290
EST:     AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|211443464|gb|FL042462.1|FL042462
EST:     AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         NCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|211443461|gb|FL042459.1|FL042459
EST:     AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|211441339|gb|FL042453.1|FL042453
EST:     AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGGTATC
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|166575936|gb|EG274034.1|EG274034
EST:     AG-AAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAG                         TCTTTGCGGCGCA
genomic: AGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCA
EST: gi|211443463|gb|FL042461.1|FL042461
EST:     GAAAAAATATTATTCTTTTGAGGAATGTATGAGNCTACCGNGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTG
genomic: GAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTAC-GTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTG

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: 594

GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 274

GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 202

GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 649

GTTGCTGTTAAGAAAATGAAGAAAAAATATTATTCTTTTGAGGAATGTATGAGTCTACGTGAAGTAAAGgtattttaga ... tttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG
                     agctgat  putative branch site (score: 649)
                                         ttatttt  putative PPT
                        tgatatttcttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttagaccagtggtgttctttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG