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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgattggcattctttttagcacaagatattatcgtcatggcctccctttttcacttgttcttttccttgtttgtcatcatgttttcaatggaaa...

Basic information

species Zea mays
transcript GRMZM2G083076_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083076_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgattg---gcattctttttagcacaagatattatcgtcatggcctccctttttcacttgttcttttccttgtttgtcatcatgttttcaatggaaa
 |||||||| ||||| |||||||| |||||||||||||| |||||||  ||||||||||| |||||||||||||| ||||| ||||||||||||||||||||||||  |||     | |||| | |  || ||||||||||   |||   |       |||| |  |  | | | |   |||   | | | ||   |      
CCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaactgcatttcctactttctatcttccataagatattatttgcattttcatggaaattcattgttgttatgcataaattgattttaagcttgggagtt---

upper sequence: GRMZM2G083076_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgattg---gcattctttttagcacaagatattatcgtcatggcctccctttttcacttgttcttttccttgtttgtca--tcatgttttcaatggaaa
 ||| | || ||||| |||||||| |||||||||||||| || ||||  ||||||||||| |||||||||||||| ||||| |||||||||||||||||||||| |  |||     |||||  | |  || ||||||||||   ||      |  | |     |  ||| ||     | | | ||   ||||  | | ||     
CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCGgtaattgcatttcttacattcgatctttcataagatattatttgcaatatgccaatatcatgttaattcattgttgggatagacaatgcatgaatgccat-----

upper sequence: GRMZM2G083076_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 5
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttg-attggcattctttttagcacaagatattatcgtcatggcctccctttttcacttgttcttttccttgt-ttgtcatcatgttttcaatggaaa
|||||| || |||||| |||||||||| || ||||| ||||| ||||  || |||||||| ||     |||||||| ||||||| ||||||||||| || |||| ||  ||||| |   || |  | | || || | |   |  |    |  || | |||    |         |    |  || | ||| |      ||  
TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGTACAAAGCTTTCTATAGAGAATGTGGAGCATCTCCTCATGAAGAGCCTATCTgtaagttctattggaag--ttctaggaaaaaaatgtgaaaattttttattttctatctcaaccatgtaaagtagtacacttccaacctgtgtatctgagatg

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|32944901|gb|CF049720.1|CF049720
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|211378395|gb|FL229425.1|FL229425
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|60342361|gb|DN209334.1|DN209334
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|78180907|gb|DV551280.1|DV551280
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|211188820|gb|FL462687.1|FL462687
EST:     CTTAGCTTTCAATCAGTGATGTGAAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|31997883|gb|CD661818.1|CD661818
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|211163793|gb|FL451880.1|FL451880
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|211378396|gb|FL229426.1|FL229426
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|149111477|gb|EE294981.2|EE294981
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|148943272|gb|EC888334.2|EC888334
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCTTCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|78103809|gb|DV522237.1|DV522237
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|60672250|gb|DN475016.1|DN475016
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|110942146|gb|EE162303.1|EE162303
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|8401221|gb|BE056855.1|BE056855
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|12047287|gb|BF729426.1|BF729426
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GGTCATCTTATTGAGGGAATAATTGATGAAGTG
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTG
EST: gi|8401231|gb|BE056865.1|BE056865
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|71325796|gb|DR799577.1|DR799577
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|211050666|gb|FL481059.1|FL481059
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCYCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|149015026|gb|EE044772.2|EE044772
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|116829258|gb|EC866181.1|EC866181
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|16377755|gb|BI992105.1|BI992105
EST:     CTCCTTATGAAGAGCCTCTCG                         GTTCTTCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|211378397|gb|FL229427.1|FL229427
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
EST: gi|37388271|gb|CF631343.1|CF631343
EST:     CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT
genomic: CTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgat ... ttaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCGgtaacttgattggcattctttttagcacaagatattatcgtcatggcctccctttttcacttgttcttttccttgtttgtcatcatgttttcaatggaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccctt