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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGCTTGTTACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacag

Basic information

species Zea mays
transcript GRMZM2G104418_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104418_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 11
TTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGCTTGTTACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgc-tgttacatct-ttttttatcacag
|||  ||||||| ||||||||||| |||||||| ||||| |||||| | ||  || | ||||| ||||||||||| || ||||||||| | ||||||||||||||    || ||| |     |||||| ||    || | |    |    |  |||    | | |      |  ||||||||  | |      ||  |||| ||||| ||    |  |||||| |   ||||     ||   |      || | |   | | || | | ||||  | | |  ||| ||| ||||  |||
TTTCTTATTTGCTGTCATGTTTGGAGATTGGGGACATGGAATTTGCATATTGGTTTCGACACTCTATCTGATAATCCGAGAGAAGAAATTTGCTTCACAGgtttgcatactggtcat-----cattttacta---ttgtgttgacaatcattttgagg--actttg-----ttctttggaatatgta---gtagtgatcccaaagagtttagagc--aagtattt---atattctgaaagccccaaaaatttaca---tatgtgataaagctgtatctgatgtctgtttcttattgcag

upper sequence: GRMZM2G104418_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 5'ss of exon 11
TTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGCTTGTTACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctcta-gtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacag
 ||||| ||||| |||||||||||||||||||| |||||  | ||||||||||| || ||| | | | | |||||  |||| ||||||||  |    |||||         | |  ||  ||| ||||  | | |   ||     | |     |    |||| ||    |      |    |||| | |  | | |||  |                                                                                                 
ATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGCTTGTTACTCGCTACATTGTTTTTTATAATCAGGGAAAAGAAACTCTCCAATCAGgtaaccagcgcatgagttagttgaatttcacattaac-attcagattttcaatgcagaacaactccttgaatcacatct--attgcagctaaatatatctcta-----------------------------------------------------------------------------------------------

upper sequence: GRMZM2G104418_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 11
TTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGCTTGTTACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtt-tgtcctctag--tcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacag
||| || ||||| || ||||||||||||||||||||||| || ||||| |||||||||||  | ||| | ||  |   ||| |||||| |  ||   |||||  ||||| || |  ||||| | |     |      || || ||| |    | | | ||| | | ||| | |    | |   ||| | |||  | ||  |                                                                                                   
TTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGCTTATTACTTGCAACCTTATATTTCATTGTCAAGGAAAAGAAATTTTCTAGTCAGgtaatgtccactggattcttgctggttaactataagcttgatatgtttcgtggaaattatagagt-ctatatc----tctcatattagtacatgcagtcataata-----------------------------------------------------------------------------------------------

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|32929086|gb|CF033898.1|CF033898
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32929323|gb|CF034135.1|CF034135
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32929184|gb|CF033996.1|CF033996
EST:     TAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGCGGGCGTTATGTAATTATG
genomic: TAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32930632|gb|CF035444.1|CF035444
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32929163|gb|CF033975.1|CF033975
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
EST: gi|32928488|gb|CF033300.1|CF033300
EST:     TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAG                         AAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG
genomic: TACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctc ... tttatcacagAAACTTGGAGACATAATGGAGATGATGTTTGGTGGGCGTTATGTAATTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGCTTGTTACTTGCAACACTTTATCTGATAATACGGGAGAAGAAACTAGCTTCACAGgtttgtcctctagtcttgattgcattttgcttcatttatctgtgtatctgtagtgatacaattctacaacctgttttggaattggaacacactgtattcccgaagagctttttacttaagtatctgggatatgtcagaacttcgttttgttaataatttctttgttcatgctgctgttacatctttttttatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA