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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcag

Basic information

species Zea mays
transcript GRMZM2G399073_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 4
GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcag
|| ||||| ||||| ||||||||  | || ||||||||||| ||| |||| |||||||||||||| |||||||| || ||||||  || ||  |||          | | |||||| ||| ||   |||||| ||| ||  | | ||| |||||||||| | |  ||   || ||
GCTTTGGACAAGATTAGGTTCCTGGCTCTCACTGATAAGGAGGTTTTGGGCGAAGGTGACACTGCTAAGCTTGAAATCCAGgtatattaaacttcgtagctgatagtcttttttgtgtggtat---atcttgttttggaaattgacttcatggcatctgctgtgggcacgtgtag

upper sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 4
-GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaatgtcgagagaccatttttcttttgtctggc--atcatatcttgctttagacttgggcttgatggc--atctgatatatgcttatgcag--
 || ||||| ||||| |||||||||||||| || |||||||| ||| |||| |||||||| |   | |||||||| |||||||| | |  | ||   |       || || |   | | | |  | ||   |  ||  |    |   | ||     |  | || | | |||||  |||    
GGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAggttagt--attgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctaca

upper sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 4
GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaatgt--cgagagaccatttttcttttgtctggcatc--atatcttgctttagacttgggcttgatggcat-ctgatatatgcttatgcag-------------------------------------------------------------------
|| ||||| || || ||||||||| | || ||||| || || ||| ||||||||||||||||||| ||||||||||| ||||| |  |  ||||  |   | |  |||||| |  |     |  |   | ||   | || |    |  | || ||   || ||||| |  |   ||  ||                                                                   
GCCTTGGACAAAATTAGGTTCCTTGCACTCACTGACAAAGACGTTTTGGGTGAAGGTGACACTGCTAAGCTTGAGATCCAGgttagctacatgtttctcaatatgatttttatgcttgagagtgttgaaaatagagtttcatcgatttgttttatcaaatgctgatctcagtaaatttagcctttcgttggaattgtgtctagtgtaagcttttttcttacctccgtaactatgctatggtatgcag

upper sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 4
GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaattt--caatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcag
||| |||||||||| |||||||||||||| || ||||||||  || | ||||||||||| |||||||||||||| || ||||| | ||   | |   |    |  | |||| | || ||| |  | |||  ||   | | | || |  ||  |   || ||||| |     ||||||
GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAGgttagttaatattactgttgtaaaaattttgtattttcttgt-ttataatttttctgacagtttgaattcttataatatgataaa-----atgcag

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|148965480|gb|EE016290.2|EE016290
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|56538364|gb|CX054073.1|CX054073
EST:     CTGATAAGAAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|149004856|gb|EE039364.2|EE039364
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|149073272|gb|EE161562.2|EE161562
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|24767582|gb|CA402726.1|CA402726
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|31360086|gb|CD444443.1|CD444443
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|148964727|gb|EC905993.2|EC905993
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
EST: gi|149112828|gb|EE295636.2|EE295636
EST:     CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG                         ATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT
genomic: CTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaa ... gcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAGgtaatttcaatgtcgagagaccatttttcttttgtctggcatcatatcttgctttagacttgggcttgatggcatctgatatatgcttatgcag

- - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG