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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtccagtggatattaataaacttattttcacctttgtctgctttggctatagatttagcacccatctagtgatctagttttcatacaagtagc...

Basic information

species Zea mays
transcript GRMZM2G375904_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375904_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 5'ss of exon 2
CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtccagtggatattaataaacttattttcacctttgtctgctttggctatagatttagcacccatctagtgatc-tagttttcatacaagtagc-------------
| || |||||||| || ||||||||||||||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||         || || | || | || ||   || |||| |||     | | ||  | | |||   || || |  |   | ||| | || | ||| |             
CGCCATCTAGTGCAACAAAACAGAGGGTTGCCGCGGCAAAACAGTACATTGAGAATCATTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAAAGgtaggc---------gacataattatatttcttgctacttttgcctg-----gttgtatttctcgcaaaaatatatttttggcattttgcgtatatgtaacggaatttgttatt
















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|211070733|gb|FL145035.1|FL145035
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAA
EST: gi|211067991|gb|FL145018.1|FL145018
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|149049840|gb|EE048527.2|EE048527
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211073467|gb|FL145044.1|FL145044
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211070726|gb|FL145028.1|FL145028
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|28873651|gb|CB329610.1|CB329610
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211067994|gb|FL145021.1|FL145021
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCCTGGATGTTGGAGAGAAAATTACAAGATGCCCGAAG
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGC-TGGATGTTGGAGAGAAAATTACAAGATGCC-GAAG
EST: gi|149070121|gb|EE158521.2|EE158521
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211067990|gb|FL145017.1|FL145017
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATACGAAAGAGAG                         GCGCTGGATGTTGGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGA
EST: gi|89250841|gb|DY622627.1|DY622627
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCCTGTAGAAG
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCC-TGTAGAAG
EST: gi|71765287|gb|DR963224.1|DR963224
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGTTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTTCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211097010|gb|FL478910.1|FL478910
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211061362|gb|FL219436.1|FL219436
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211073466|gb|FL145043.1|FL145043
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211070727|gb|FL145029.1|FL145029
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAANGATGCCGAAGTTCCTGTANAAG
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAA-GATGCCGAAGTTCCTGTAGAAG
EST: gi|211070738|gb|FL145040.1|FL145040
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|213183785|gb|FM191845.1|FM191845
EST:     GAGAACCACTACAAGACCCAGANNNAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211073464|gb|FL145041.1|FL145041
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211073468|gb|FL145045.1|FL145045
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211067998|gb|FL145025.1|FL145025
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211070735|gb|FL145037.1|FL145037
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211070729|gb|FL145031.1|FL145031
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211070730|gb|FL145032.1|FL145032
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211067996|gb|FL145023.1|FL145023
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCCGAAGTTCCTGTAGAAN
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCC-GAAGTTCCTGTAGAAG
EST: gi|211070736|gb|FL145038.1|FL145038
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211067989|gb|FL145016.1|FL145016
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTANAAGA
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGA
EST: gi|211070725|gb|FL145027.1|FL145027
EST:     AGAACCACTACAAGACCCAGNATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTTGGATGTTGGAGAGAAAATTACAAGATGCCCGAAG
genomic: AGAACCACTACAAGACCCAG-ATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCT-GGATGTTGGAGAGAAAATTACAAGATGCC-GAAG
EST: gi|211067995|gb|FL145022.1|FL145022
EST:     GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAAATTACAAGNATGCCGAAGTTCCTGTANAAG
genomic: GAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAG-ATGCCGAAGTTCCTGTAGAAG
EST: gi|211195287|gb|FK977678.1|FK977678
EST:     AGAACCACTANCA-GACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAG                         GCGCTGGATGTTGGAGAGAAA-TTACAAGATGCCCGA-GTTCCTGTAGAAG
genomic: AGAACCACTA-CAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCC-GAAGTTCCTGTAGAAG

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), 48 (downstream exon)
Score: 354

CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGAGCAAAATAACATTCTTAAGCATTTGGAGAAAAAAGAGACTGAATATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 511

CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGAGCAAAATAACATTCTTAAGCATTTGGAGAAAAAAGAGACTGAATATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 520

CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGAGCAAAATAACATTCTTAAGCATTTGGAGAAAAAAGAGACTGAATATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 853

CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtc ... ttacttttagGCGCTGGATGTTGGAGAGAAAATTACAAGATGCCGAAGTTCCTGTAGAAGAGCAAAATAACATTCTTAAGCATTTGGAGAAAAAAGAGACTGAATATATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCTTCTAGTGCGACGAAACAGAGGGTTGCCGCTGCAAAACAGTACATTGAGAACCACTACAAGACCCAGATGAAGTCCCTGCAAGATAGGAAAGAGAGgtaggcagtccagtggatattaataaacttattttcacctttgtctgctttggctatagatttagcacccatctagtgatctagttttcatacaagtagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA