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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatgttgtctctgcttttgattatccttcgcagcagggagcagtgatatgtttttctgtgaaatgatgcctacattgggtcgctgaattccattgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 26
AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg-ttgt-ctctgcttttgattatccttcgcagcagggagcagt-----gatatgtttttctgtgaaatgatgcctacattgggtcgctg-aattccattgtgtgcag-----------------------------------------------------
||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||||||   || || |||| |  |||| |  | |      |     |  |     |     | | | |  |    | | |||    |   |||      ||  ||||  | |||     |                                                     
AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattgcttgtaccttgctgtcaactgaagacctagataaagtttgttttttgggtttatgctgtctttagatgcactccttattcttctactacaattatactgttaagtgacaacgctttttattttatatgctaatatggggttcgcttcctttctattcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 17
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 25
AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatgttgtctctgcttttgattatccttcgcagcagggagcagtgatatgtttttctgtgaaatgatgcctacattgggtcgctgaattccattgtgtgcag
|||||||||||||||||||| ||||  || || |||||||| || ||||| |||||||||||       |||     |   |  ||||     ||| | |  | ||      ||  ||  ||    || | || | |    |   ||      ||   |||  | |||
AATCTGTGTGTGACCGCAGCACATTTTCCAATCCGAGAAATACTGGAGAAAGAAAAGAAGgtttg----gtttctgtttaatgcgattgcttctcgaatcctgaagtccatttacattactcgcataactcattctttttattattctggctgttgttttgactacag
















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|71763086|gb|DR961023.1|DR961023
EST:     TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGA
genomic: TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGA
EST: gi|67025653|gb|CO454402.1|CO454402
EST:     TGACCGCAGCGCATTACCC-ATTCGAGAA-TCCTANAGAAG-AAAAGAAA                         GAGAAGAGTT-GGCTAAA-CAGAAG-TAGGC
genomic: TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGC
EST: gi|9794440|gb|BE552748.1|BE552748
EST:     ACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGATATTTGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGG
genomic: ACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGA-A-AAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGG
EST: gi|71435056|gb|DR816106.1|DR816106
EST:     TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCGTTGTATGGA
genomic: TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGA
EST: gi|16925353|gb|BM078421.1|BM078421
EST:     TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAG                         GAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGA
genomic: TGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGA

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), 48 (downstream exon)
Score: 192

AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGAAGCGAGCACATCCGTCCTCTTAGCATAGACGACTTCAAATCCGCCCATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 220

AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGAAGCGAGCACATCCGTCCTCTTAGCATAGACGACTTCAAATCCGCCCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGAAGCGAGCACATCCGTCCTCTTAGCATAGACGACTTCAAATCCGCCCATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 223

AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg ... ttgtgtgcagGAGAAGAGTTTGGCTAAAACAGAAGGTAGGCCAGAGCCCGCATTGTATGGAAGCGAGCACATCCGTCCTCTTAGCATAGACGACTTCAAATCCGCCCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatgttgtctctgcttttgattatccttcgcagcagggagcagtgatatgtttttctgtgaaatgatgcctacattgggtcgctgaattccattgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG