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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag

Basic information

species Zea mays
transcript GRMZM2G447433_T08
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g27040.1 (Oryza sativa), 5'ss of exon 7
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatgga----gtgtcattctcttatttc--ttttcag
 |||| ||||||||||||||||| ||||| |||||||| || ||||||||||||||||||||||||||||||||||| || ||||| || ||||| ||||||||| || |  |||| ||  || | |    | ||||| |||||| || |    ||| ||   |  ||||||    || |||||||  | |  |  |||||||
ATAGTATTTCTGCCTCTACTTGTTGCGTCCCTTGTGGCAGTCTCTCGAGTTGATGATTACTGGCATCACTGGCAAGACGTATTTGCAGGTGGCATTATAGgtttgttatt--ttgaagcctttctct--caaccatttagaacactct-cgttgtcagaaagtaggcatggatctcgtctcattcttctttcccctttttcag

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 6
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagt--gtcattctcttatttcttttcag
 |||| ||||||||||||||||| || ||||||||||| || ||||| ||||| |||||||||||||||||||||||||| ||||| |||||||| |||||| || |||| ||  | |||  | ||||     || ||  ||||  |||  |  |||| |      |||| | |   ||    |||      | |||||
CTAGTCTTTCTGCCTCTACTTGTTGCATCACTTGTGGCAGTCTCTCGGGTTGACGATTACTGGCATCACTGGCAAGATGTATTTGCAGGCGGCATTATAGgtctg-tagt-ttcaacgct--tctgtac----cactttaaacattctt-gctctcaagataagtacatgtaattcatctcattctctaccttattcag

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G18450.2 (Glycine max), 5'ss of exon 6
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag
 | |||||  | || || ||||| ||  |  |  | ||||| ||||| ||||||||||| |||||||| ||||||||||| ||| | || ||  | |||||| || |      ||  | | || | | |||    | |  |      |    ||  | |  |   ||  |   | | || |      || | | |||
ATTGTTTTCTTTCCGCTTCTTGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTTTTTACTGGAGGGCTTATAGgtctgttgaagactg--gattttctttgtttgatttattaa------tatgtaaatatacttttctccagactttttatacg--agcttttatgcag

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G25650.1 (Glycine max), 5'ss of exon 6
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcga-acacccttcacaatcaaaagtcaatcatg-gagtgtcattctcttatttcttttcag
 | |||||  | ||  | || || ||  |  |  | ||||| ||||| |||||||||||||||||||| ||||||||||| ||||| || |   | ||||||||| |       || ||    ||| |||    ||||| | | ||||||     | ||||||   | ||  || |||| ||  |              
CTTGTTTTCTTACCAATCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTACTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTTATAGgtttgtt---tcccgaagccagattg-attatatatttcaataaacccttt----tgaaaagtttctgatacgaatgtcttttaccag-----------

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G41580.1 (Glycine max), 5'ss of exon 6
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcga-acacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag
 | |||||  | ||  | || || ||  |  |  | ||||| ||||| ||||||||||| |||||||| ||||||||||| ||||| || |   | ||||||| | |      ||||||    ||| ||| |  ||||| | | ||||||  ||   ||   ||    | | |   |  || |   |           
CTTGTTTTCTTACCATTCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTAATAGgttagtttac---tgatgccagattg-attaaatatttcaataaacccttttca---aagtttctgatacgaatattttttttaccag----------

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: AT1G15080.1 (Arabidopsis thaliana), 5'ss of exon 6
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag
 | ||  || | |||||||| || ||  || | || | ||| ||  |||||||||| || |||||||||||||||||||| ||||  || |  |||||||||||| | || ||   ||   ||||  | | |  | ||| ||    | | | || |||| |   || |  ||    |||  |  |     | | |||
ATTGTGATTTTACCTCTACTGGTTGCAGCATTGGTTGGTGTATCCAGAGTTGATGACTATTGGCATCACTGGCAAGATGTTTTTGGAGGAGCTATCATAGgtttgtttgtttt---tgtcttttttaactcatgaattcaaaattacgtgagaaacaaa-gctgatgacagacacacatctttcttgcaatgtccag

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 8
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 5'ss of exon 5
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgct-----agtatt--tgatgctcttttgtatttagcatttcga-acacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag---
 | ||||| |||||  ||||| | ||  | || ||||  ||||||||||| ||||| || |||||||||||||||||||| |||||||| ||  | |||||| || |     ||||    ||||  |   | | || |  | || |   ||    |||  | | | |      ||   |  |     | | |  || || |   |   
ATTGTTTTCCTGCCCATACTTCTTGCAGCTCTAGTGGGAGTTTCTCGAGTAGATGACTATTGGCATCACTGGCAAGATGTATTTGCCGGAGGTGTAATAGgtctgttttatcagtaccgatgattatgaatggaatctttccttactctacttttttctgatttatacactcttctcagtataattctttgtccttcctctctggcag

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|101397318|gb|EB820582.1|EB820582
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|16917409|gb|BM073273.1|BM073273
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|71332341|gb|DR803110.1|DR803110
EST:     CTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: CTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|211272973|gb|FL366561.1|FL366561
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCT
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCT
EST: gi|211457273|gb|FL438512.1|FL438512
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|60357163|gb|DN224136.1|DN224136
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|71762628|gb|DR960565.1|DR960565
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|71332342|gb|DR803111.1|DR803111
EST:     CTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: CTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|18166760|gb|BM336599.1|BM336599
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|60350401|gb|DN217374.1|DN217374
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
EST: gi|18167942|gb|BM337782.1|BM337782
EST:     TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAG                         GTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG
genomic: TGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagt ... ttcttttcagGTCTTACAGTTGCTTCATTCTGTTACCTGCAGTTCTTCCCATATCCCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGTTTTTCTGCCTCTACTTGTCGCGTCACTTGTGGCTGTTTCTCGAGTTGATGATTACTGGCATCACTGGCAAGATGTCTTTGCCGGCGGCATCATAGgtttgctagtatttgatgctcttttgtatttagcatttcgaacacccttcacaatcaaaagtcaatcatggagtgtcattctcttatttcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG