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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcctcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgttaactcatctcgtggcatcgtaattgcag

Basic information

species Zea mays
transcript GRMZM2G069631_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 11
CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcctcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgttaactcatctcgtggcatcgt-aattgcag
|| |||||| |||| || || |||||||| |||||||||||||| || || || || || |||||||| | |||||||||||| ||||| |||||| | ||| | |||  | |||||| |   |     |||| || ||   || ||||   ||  || |||||||||||  || ||||   | | || |||||
CTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAGgtatctgcttgttctc--attatgagttaccaatgccgctaactattat-tttatttggaactactatatgttaactctccttgtggtgccttcaactgcag

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 11
CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcctcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgttaactcatctcgtggcatcgtaattgcag
|||||||||||||| || || |||||||||||||| || |||||||| || || || || |||||| | | |||| ||||||||||||| ||||||      |  ||    ||||   ||||| |   ||  |  | ||| ||    ||   ||   | | | | |  | ||  |                  
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAGgtatggatacaaacttaatctat---ctgtg-gttctgtca-ttcttgagtctgcttcttactattttgtttcatttgataccag----------------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 11
CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcctcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgttaactcatctcgtggcatcgtaattgcag
|||||||||||||| || || |||||||||||||| || |||||||| || || || || |||||| | | |||| ||||||| ||||| ||||||    |||       ||| | | || |  |   | || | | ||   || |     || ||   ||| ||   |||| |  |  ||            
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatta-----aaact-taatctatatgtggttct-gttatt--cttgagcctgcatcttactattttgtttcatttgattccag-----------

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 11
CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcc--tcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgtt----------aactcatctcgtggcatcgtaattgcag----------------------------------------
||||||||| | ||||||||||| || ||||| ||||| |||||||| || || || ||||||||    | |||||||||||||||||| |||||| |  || | |   |  |   |  | || | | |      |   |  ||  ||||||  |    |  |||||           | | |  |   | |||  |  |                                             
CTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAGgtattttgtttttcagccaaatagttcgatgggtggaacttatggaatatggcacatttagaatgcatcaatgttttgtttctacgatttactttaggacatttttgtgatgtcttgtaaagagattacaactgaactattcctttgtcacag

upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 5'ss of exon 11
CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcctcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgttaactcatctcgtggcatcgtaattgcag
||||||||||||||||||| ||| ||||| |||||||| |||||||||||||| || || ||||| || |  ||||| |||||||||||||||| | |     | |    | |     |    | | || |    ||  |   |   ||   |  |  | |  |||       | ||   | || |  |  | 
CTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAGgtttgttacatttcgaaaaattacttccagcatagttccagaatggggtcgttgctttttaaatgcgcagattagtgtcggttgtttaagcggaggtaga-

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|71772340|gb|DR970276.1|DR970276
EST:     CAACTGGTTCTTATAG                         TAATTTGTTTCGTGTTTTTGGTTGTT-TCCTGAAAGCGTGGAGGCATCAAC
genomic: CAACTGGTTCTTATAGgtatatcctt ... gtaattgcagTAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAAC
EST: gi|211227826|gb|FL399539.1|FL399539
EST:     GAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG                         TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAAC
genomic: GAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatcctt ... gtaattgcagTAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAAC
EST: gi|71772341|gb|DR970277.1|DR970277
EST:     GAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG                         TAATTTGTTTCGTGTTTTTGGTTG
genomic: GAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatcctt ... gtaattgcagTAATTTGTTTCGTGTTTTTGGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAGgtatatccttatcctcgcactatgagctgtgagaattgctagctgttgggttcatttaacacctctgtatgttaactcatctcgtggcatcgtaattgcag

- - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA