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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTTTGAGACTCAAGCAAAATGGTTACTCTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataaatgttgtcttttatgttttgcatgcttactaaaccatcaattgctaatccacatcgcaattttttagattgtcaacctgttatatgacac...

Basic information

species Zea mays
transcript GRMZM2G149802_T01
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149802_T02 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os01g64820.1 (Oryza sativa), 5'ss of exon 23
GTTGCTTTGAGACTCAAGCAAAATGGTTACTCTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaata--aatgttg-tcttttatgttttgcatgcttactaaaccatcaattgctaa-tccacatcgcaattttttagattgtcaacctgttatatgacac
|||||||| ||||| |||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||||||||||| ||||||||||    | || || ||  ||   || | ||||    || |  |  |  ||| ||| |    | ||| |  || || |   |  ||    ||  ||  | 
GTTGCTTTAAGACTGAAGCAAAATGGTTATTCTGGGTGCTCTGCAGGTGATACAGTTCCCTATATAATTTGCTCTCAACAGgtattaaatgcattgctggtccattggtttattcatgggccctcatactcc--ttgttaagttgttagcgccaacttgtataactttgac--actaattggtag

upper sequence: GRMZM2G149802_T02 (Zea mays), 5'ss of exon 23
lower sequence: GLYMA01G39430.1 (Glycine max), 5'ss of exon 24
GTTGCTTTGAGACTCAAGCAAAATGGTTACTCT---GGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtat-taataaatgttgtcttttatgttttgcatgcttactaaaccatcaattgctaatccacatcgca-attt----tttagattgtc--aacctgt-tatatgacac-------------------
|| ||    ||| | |||||| | || ||||||   |||||||| | |||||| ||| | |||||||||||||||| | ||||||| | | ||  |     |||   |      |      || |  | | |       |  |   |||||   ||||    | ||  |||||  ||  ||| | | | | |                    
GTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGTGATACAATCCCTTATATAATTTGCTATGAGCAGgtttgtcatttagtcactctcccaatcaaaggccaaatagtgcaactttgggaaattttttgcatcgagtatttggtgtatatgttgtctcaatttgtatttttaatattatgttctgctttgattag

upper sequence: GRMZM2G149802_T02 (Zea mays), 5'ss of exon 23
lower sequence: Vv07s0031g00470.t01 (Vitis vinifera), 5'ss of exon 22
GTTGCTTTGAGACTCAAGCAAAATGGTTACTC---TGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgt-attaata-aatgttgtcttttatgttttgcatgctt---actaaaccatcaattgctaatccacatcgcaattttttagattgtca-acctgttatatgacac-------------------------------
|| ||  | ||| | ||||||| |||||||||   |||||||||||||||||| ||||| |||||||| ||||||| | |||||||   ||||  |   |||  |||| | |   | | ||     |  ||||  |    | ||   |  | ||   || ||| ||||| | | |  ||| ||| |                                   
GTGGCACTAAGATTGAAGCAAAGTGGTTACTCAACTGGTTGCTCAGCTGGTGATACAGTCCCTTATATTATTTGCTGTGAGCAGgttggtaatgcagcattgcattttctatggaggaagcagtaaatcaaactttggcgtactgggcttcttct--atgtttaagatttttacatttgtaataagtttttgagctttacttttttcttgtgtgtggacag

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|32939296|gb|CF044115.1|CF044115
EST:     ACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: ACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
EST: gi|32938785|gb|CF043604.1|CF043604
EST:     GTACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: GTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
EST: gi|211402399|gb|FL354720.1|FL354720
EST:     CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
EST: gi|32938920|gb|CF043739.1|CF043739
EST:     ACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: ACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
EST: gi|74242013|gb|DT649927.1|DT649927
EST:     CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAG                         GACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC
genomic: CTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataa ... taccgtacagGACTCAGATAATGCACATTCTGTGGGAATAGCTCAGAGAGCTAGACATCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTTTGAGACTCAAGCAAAATGGTTACTCTGGTTGCTCAGCTGGTGACACAGTACCTTATATAATTTGCTCTCAGCAGgtattaataaatgttgtcttttatgttttgcatgcttactaaaccatcaattgctaatccacatcgcaattttttagattgtcaacctgttatatgacac

- - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - CAGCTG