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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacacagctccatactctgcttacctttggcattttgctattgttgtgtttattggtttagattcaagaatgccaattttcttaacaatgaagac...

Basic information

species Zea mays
transcript GRMZM2G044819_T03
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 5'ss of exon 17
ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacacagctcc--atactctgcttacctttggcattttgc--tattgttgtgtttattggtttagattcaagaatgccaattttcttaacaatgaagac
||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||||||||||| | || | |||   ||  | |  || |||||  | || | |  | || |  |  | |||      |||| |    ||  | || | ||  |  | ||   
ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAGgtaattgcaaaactctagatgatttatttcccttttaccttctacatttttatcatagtcatttcgactgattgagacctgatatttctgtttcct-taaa---

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA13G17950.1 (Glycine max), 5'ss of exon 16
ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacacagctccatactctgcttacctttggcattttgctattgttgtgtttattggtttagattcaagaatgccaattttcttaacaatgaagac
|||||||||||| || ||||| ||||| ||||||||| || | ||||| || |||||||||||||  ||||| |||||||||   | |    |   |  | |  | |  |   |||||  | ||||||| ||  | |    |  || | |   ||||   || | |   |  || ||  
ATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAGgtattcagatgagt--gttttttaatcatataaagcattaggttattgttttgactttaaact--gacttagatatgc---ttctttgtgctctgcag--

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA17G04580.1 (Glycine max), 5'ss of exon 16
ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacacagctccatactctgcttacctttggcattttgctattgttgtgtttattggtttagattcaagaatgccaattttcttaacaatgaagac
|||||||||||| || ||||| ||||| ||||||||| || | ||||| || |||||||||||||  ||||| |||||||||   | |   ||   |  | |  | |  |   ||||   | ||||||| ||  | |    |  || | |   ||||   || | |   |  || ||  
ATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAGgtattcagatgact--gttttttaatcatataaagcataaggttattgttttgactttaaact--gacttagatatgc---ttctttgtgctctgcag--

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 5'ss of exon 16
ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacacagctccatactctgct-tacctttggcattttgctattgttgtgtttattggtttagattcaagaatgccaattttcttaacaatgaagac---
 ||||||||||| ||||| || ||||| |||||||| || || ||||| || || |||||||| || || || ||||||||  || || ||    ||    | ||  | | |      | |  | || ||      |||   ||  ||  ||  | |    |      ||  |  |||     
GTATGCTGATATTTACACCTCTAGGGTCTCAAATTTCCTACATTATACACCCTTTATGTATTTTCACTCACAGGAACAGgt--attcagagtattatggctttctgcatcatattttctgtcttgtttttacccccattatattgcat--aaataggtaggtcacgacaaggacaaagggcgt

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|32834655|gb|CD974333.1|CD974333
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCG-CATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGT
EST: gi|78025583|gb|DV493970.1|DV493970
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|5713778|gb|AI943770.1|AI943770
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|211089552|gb|FL477198.1|FL477198
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|166645329|gb|EG101675.1|EG101675
EST:     CAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|211089553|gb|FL477199.1|FL477199
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|148967092|gb|EE018262.2|EE018262
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTTTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|5688498|gb|AI941513.1|AI941513
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|211502877|gb|FL438187.1|FL438187
EST:     ACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: ACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|12973741|gb|BG268632.1|BG268632
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
EST: gi|166487459|gb|EG163127.1|EG163127
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGACGCATGATGCCC
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTG-CGCATGATGCCC
EST: gi|16917596|gb|BM073359.1|BM073359
EST:     CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG                         ACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT
genomic: CAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacac ... attgtctcagACACTTGCGCATGATGCCCATTCCTATTCTGGAGGAAAGGACATCAAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAGgtaaatacacagctccatactctgcttacctttggcattttgctattgttgtgtttattggtttagattcaagaatgccaattttcttaacaatgaagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC