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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt...

Basic information

species Zea mays
transcript GRMZM2G091119_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgcaatggttat-gttgcaaatgagtgt----
|||||| | | | |||||||| || | |||||||||||| ||||||||||| |||||||| |||||||||||||||||||| |||||||||||||||||||||   |   |  || | ||    ||       |  | |   ||    | |   |        |||| | | |||||    |  | |||  || || ||      
CCTCCTAAGTCTGTTGACACAAAATCTCAAGAAAAGCATCAAGAAAGAGGCTTGCTGGACTATTTCAAATATTACTGCTGGTAACAAAGATCAGATACAGgta---tgtgtacagacttaaaaaatactgacatgctcatcattct--actaagtcatgaaggatttgtgtagtgcatacttagtagttttaattgtgttccctc

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G04430.1 (Glycine max), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaattt-ctctggtgcaatggttatgttgcaaatgagtgt-----
|||| |||   | |||||||| || || || ||||| || |||||||| || |||||||| |||||||| ||||| |||||||||| |||||||||||||||||     |  || ||| |    || |  || || ||   || | | ||||  |   ||||| ||| || | |     || |   |||     |   | |     
CCTCTTGAGCCTGTTGACACATAATCATAAAAAAAGTATCAAGAAAGAAGCTTGCTGGACCATTTCAAACATTACAGCTGGAAACAGAGATCAGATACAGgtaagccggt--aaatccca----attagattttacttgatgtaaattagtgtgtttgatcaagtttgctattgcctgttgatctcgttttttttttctttcttaa

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G37180.1 (Glycine max), 5'ss of exon 9
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtg-gatggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt
|||  ||||  | |||||| | || || || |||||||| |||||||| || || ||||| || ||||| |||||||||||||| ||||| |||||||||||||   |    |   |   || ||    |||   | ||  |||  |    |  ||    |    ||      |   |   ||||  ||| || ||| |  
CCTTTTGAACCTGTTGACAAATAATCATAAAAAAAGCATCAAGAAAGAAGCTTGTTGGACCATATCAAACATTACTGCTGGAAATAAAGAACAGATACAGgtaaaccagcaaatcccaattgtcactgtttttattatagggttttttctggtaattttgttgtcttgaatctgcatacatgttaaattg-aattgattca

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G15480.1 (Glycine max), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgc-----aatggttatgttgcaaatgagtgt-
|||| |||   | |||||||| || || || ||||| || |||||||| ||||||||||| || ||||| ||||| |||||||||| |||||||||||||||||     |  || ||| |    ||   ||  || ||   || | |   ||  |   |||||   |   |  |||      ||  || | || |   | ||| | 
CCTCTTGAGCCTGTTGACACACAATCATAAAAAAAGTATCAAGAAAGAAGCATGCTGGACCATATCAAACATTACGGCTGGAAACAGAGATCAGATACAGgtaagccggt--aaatccca----attgtttgttacttgatgtaaattcttgtgtttaatcaagccttcttactgccaattgatcttttttttccctttaagtttg

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA17G03430.1 (Glycine max), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggca-tcaaatttctctggtgcaatggttatgttgcaaatgagtgt---
|||  ||||  | |||||| | || || || ||||||||||||||||| || || ||||| || ||||| |||||||||||||| ||||| |||||||||||||   |    || ||| |     | | | | | |||  |     |  ||   ||| | |    ||    ||   |       |||||  || ||| |     
CCTTTTGAACCTGTTGACAAATAATCATAAAAAAAGCATTAAGAAAGAAGCTTGTTGGACTATATCAAACATTACTGCTGGAAATAAAGAACAGATACAGgtaagccagc--aaatccca-attgtcactgtatgtttttataggttttgtttttggtagttttgttgtcttgaatctgcatacatgtta-aactgaattgatt

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT3G06720.2 (Arabidopsis thaliana), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaattt-gtatttacagttactaagtggatggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt--
 ||    ||  |  | || || ||||| ||||||||||| ||||| || || ||||||||||||||||| || || || || |||||||||||||| ||||||    | | | | |  |    |||   ||| |||         |   ||        | | |  |||  |  |    | ||| |    |  |||  ||   
TCTTGCCAACCTGCTCACTCAAAACCATAAGAAAAGCATAAAGAAGGAAGCTTGCTGGACGATTTCAAACATCACAGCAGGCAACAAAGATCAGATCCAGgtaggcaattagtactgtttcatcatatgttttgtaccgtttcccatccagacttctataccta--ttcattaattgtgttgtttttcccctgatggttgcag

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0005g01100.t01 (Vitis vinifera), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagt-cctatgccatg-aatttgtatttacagttactaagtggat--ggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt
|||  ||||  | ||| |||| ||  ||||||||||||| ||||| ||||| |||||||| || ||||| || || |||||||| ||||||||||||||||| |   | | ||     || || ||   ||  |||  ||   | |  ||||   ||  ||| ||    ||||    |||     |||| ||||   ||| |||
CCTTTTGAACCTGTTGTCACATAATTACAAGAAAAGCATCAAGAAGGAGGCTTGCTGGACCATCTCAAACATCACAGCTGGAAATAAAGATCAGATACAGgtga-gcagtagattcatctgtggcaaacaaactgtgcttcatgattttaaggatataaggcttcttgattcttatttgccgcccttattttgc---tgattgt

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt-----
||| |||||  | |||||  | ||||| ||||| ||||| ||||| || || || ||||| ||||||||||| || ||||| ||||| || ||||| |||||||  ||   ||       |    | ||  ||   |      | |    |   ||||||  | |   | |  |  | |||   ||  | | ||  |||      
CCTTCTGAACCTGTTGACCAATAACCATAAGAAGAGCATCAAGAAGGAAGCTTGTTGGACTATTTCAAATATCACAGCTGGCAACAAGGAGCAGATTCAGgtaatctaag-gattcttctttttttaaacatgcgatcctgagtgc---atttttggcattca-tggttttaataaattggaactgcagtatatatgtgaatgtg

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv05s0077g01430.t01 (Vitis vinifera), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgc-aatggttat--gttgcaaatgagtgt
||| ||||   | ||||| || || || || || ||||| |||||||| || |||||||| |||||||||||||| ||||||||||| || ||||| |||||||    |  | |  |||  |  ||  | |     |||   ||| ||  ||| | |  |  ||      ||  ||      ||||  | ||||||    |  
CCTTCTGAGCCTGTTGACCCATAATCATAAAAAGAGCATCAAGAAAGAAGCTTGCTGGACTATTTCAAATATTACAGCTGGAAACAAGGAACAGATCCAGgtaa---gcaagtacaccttggaaatttaatgcctcttagctttattatttggtttgattttaaggaacttgtagctggcttttattggctgcaaaattttcc

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S230_50V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcc--tatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgca-atggttatgttgcaaatgagtgt------------------------------
 ||||||  | |  ||||  | || ||||||||||||||||||||||| || || ||||| ||||| || || || || |||||||| |||||||| ||||||  |   |  |    |  ||| | ||   | |  |||     || ||   |   |  ||      ||| |||       | || ||  |   |||   |||                              
TCTCCTGGCTCTCCTGACCAACAATCACAAGAAAAGCATTAAGAAAGAAGCTTGTTGGACTATTTCGAACATAACCGCAGGAAACAAGGATCAGATTCAGgtattaatttccactctccttattcaatccctgttgattggagattgcttt-tattttccactcctgttcactgcactgtgtagtcatacttttaattgatgtactataatcgttttcggttgtctactacag

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaaca-tacttgaagtcctatgccatgaatttg----tatttacagttactaag------tggatggca-tcaaatttctctggtgcaatggttatgttgcaaatgagtgt
 || ||   | |  ||||  | || ||||||||||| || |||||||| || || ||||| ||||| ||||| ||||| |||||||| ||||| || ||||||| | || ||    |  | ||  |    ||      ||||||    |   | |      ||  ||    |   | |    |  | || || ||   | |    |  ||  
TCTTCTTGCTCTTCTGACCAACAATCACAAGAAAAGTATCAAGAAAGAAGCCTGTTGGACTATTTCCAATATAACTGCAGGAAACAAGGATCAAATCCAGgtaaaaatatttttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtag

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S165_51V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgc-catgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt---------------------------------------
||| ||     |||||||  | ||||||||||| |||||||||||||| ||||| ||||| || || || || ||||| ||||||||||| || || |||||   ||   | |  || | ||| ||| | ||| | ||    |||     ||  || |  |  || |||        | ||||| ||||   |||    |                                        
CCTGCTCGCACTATTGACCAACAACCACAAGAAGAGCATTAAGAAAGAAGCATGTTGGACTATCTCCAACATCACTGCCGGAAACAAAGAGCAAATTCAGgttggat-tgtaatttcgtctgcgcattagtttctgttcgttgtt-----gtcaataggtttgaagttcgtcaaaata-tggttctgttctgaatattggctctggcaccccatgactaaagctcctgtacattccgcag

upper sequence: GRMZM2G091119_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S43_141V6.1 (Physcomitrella patens), 5'ss of exon 9
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatt-tctctggtgcaatggttatgttgcaaatga-gtgt--------------
 || ||   | |  | ||  | |||||||||||||||||||| || || || |||||||| || || || || |||||||||||||| ||||||||   |||| |  |||  || || | | | ||||  |   | ||   |||   |  ||| |||   |||    ||  |     | |||| ||||| |  |||  |||               
TCTTCTCGCTCTTCTCACCAACAACCACAAGAAAAGCATTAAAAAGGAAGCCTGCTGGACTATCTCCAACATCACTGCTGGAAACAAGGATCAGATTATGgta-cgaactcaaaatc-tgttctatga--tcaaactt-tggtttagatttggttggtcccaatcaatccttaactgagtggtaatgttactgatgtcgtggattattttctgcag

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|211478265|gb|FL127102.1|FL127102
EST:     CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAG                         GCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
genomic: CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatact ... gaatttttagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
EST: gi|32856329|gb|CD996010.1|CD996010
EST:     CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAG                         GCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
genomic: CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatact ... gaatttttagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
EST: gi|211478267|gb|FL127104.1|FL127104
EST:     CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAG                         GCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
genomic: CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatact ... gaatttttagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
EST: gi|60397633|gb|DN230449.1|DN230449
EST:     CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAG                         GCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
genomic: CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatact ... gaatttttagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
EST: gi|211481132|gb|FL127105.1|FL127105
EST:     CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAG                         GCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA
genomic: CATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatact ... gaatttttagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCCTGAATTTATTGACACAGAACCACAAGAAAAGCATTAAGAAAGAGGCATGCTGGACGATTTCAAATATTACTGCTGGAAACAAAGATCAGATACAGgtaacatacttgaagtcctatgccatgaatttgtatttacagttactaagtggatggcatcaaatttctctggtgcaatggttatgttgcaaatgagtgt

- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA