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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatgaaattacttggtatataatgttcattatgcttcttgtggttatcttgatatgttatagtggtttattgttccactatcttgggatgtagt...

Basic information

species Zea mays
transcript GRMZM2G447433_T08
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g27040.1 (Oryza sativa), 5'ss of exon 6
AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatgaaattacttggtatataatgttcattatgcttcttgtggttatcttgatatgttatagtggtttat-tgttccactatcttgggatgtagt
|| ||| ||||| | || ||  |||| ||||||||||||||||||||||| ||||||||||| || ||||| || ||||||||||||||||||||||||| ||| ||    | ||||  |     |  | | |   | |    |  |  |||  || ||| | | ||||  ||     | |  |     | |   
AAGTTTGATAATGTCACTACAAATGTCATATGCCATGGAGAAAAGAGTGTTATCAAGGAAGGCCACAAGAGCTTTCCAAGTGGGCATTCTTCATgtaagacatgcaacgcatcggtacttttaagttttgaagtaccgttgtatgtttctgagttgatatcgagctttacatgccttgcaacatgcatttttta-

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g27030.2 (Oryza sativa), 5'ss of exon 5
AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatgaaat-------tacttggtatataatgttcattatgcttcttgtggttatcttgatatgttatagtggtttattgttccactatcttgggatgtagt
||||| |||||| | ||    ||||| |||||||||||||||| ||||||||||||||||||  | ||||| ||||||||||||||||||||| |||| |||             ||||    |||| ||||   ||||||||     |||| | ||  | ||   | ||   |||    |     || ||   || | | 
AATTTCAATAATGTCACTGGTGATGTCATATGCCATGGAGAAAGGAGTGTCATCAAGGAAGGCTACAAGAGCTTCCCAAGTGGGCATTCTTCAGgtaataaacagtgcacagttgtactctagatatgatgtc--ttatgcttta---ggttttttttttttgaagttgtaacttaactgtaagtaattttctcat-tgg-

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g03170.t01 (Vitis vinifera), 5'ss of exon 4
AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatgaaattacttggtatataatgtt--cattatgcttcttgtggttatcttgatatgttatagtggtttattgttccactatcttggg-atgtagt
   ||| ||  | |||| |   |||| || || |||||||| ||| |||| || |||||||| || || |||||||| ||||||||| ||||||||||| |    |  |||     ||     | |  ||| |   | ||| |       |||||     || |     | |  ||  |   | ||||| || |   
TTGTTTGATCCTCTAACAAAGAATGTCATCTGTCATGGAGACAAGGGTGTTATAAAGGAAGGACACAAAAGTTTCCCTAGTGGGCATACTTCATgtaagtagaacatctaccacagatgatcggataacatgactatgcttatcagatggttgattgagcatggcatcatttacttggagagtgttgggcatat---

upper sequence: GRMZM2G447433_T08 (Zea mays), 5'ss of exon 7
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 5'ss of exon 4
AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatgaaattacttggtatataatgttcattatgcttct-tgtggttatc-ttgatatgttatagtggtttattgttccactatcttgggatgtagt
   ||| | | || ||| || |||||  | ||   |||||| || ||||||||||||||||| ||||| |||||||| ||||||||| |||| ||||||  |   | |||||  |   |   | | |  | |     | | |||||    ||| ||  ||   | |  ||  | ||    |   |    |  |   
GTGTTTGACACTAGAACAACAGATGTTCTGTGTACTGGAGACAAAAGTGTCATCAAGGAAGGACATAAAAGTTTCCCTAGTGGGCATACTTCTTgtaagtgaccta-ttactgtgggaactgtatgctgtgtatcaatatatggttcctgttgctagtttccggagcatttcttttttcatgcatgaatacatga-

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|211211372|gb|FL470796.1|FL470796
EST:     GAGTGTCCTCAACGAAGGTCACAAGAGTTTCCCCAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCCTGCATGGTACCTGGCTGGCAAACTTA
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
EST: gi|211272973|gb|FL366561.1|FL366561
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
EST: gi|10697618|gb|BE997342.1|BE997342
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
EST: gi|32932160|gb|CF036972.1|CF036972
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTAC
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTAC
EST: gi|60357163|gb|DN224136.1|DN224136
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
EST: gi|71762628|gb|DR960565.1|DR960565
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
EST: gi|32932582|gb|CF037394.1|CF037394
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGT
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGT
EST: gi|60350401|gb|DN217374.1|DN217374
EST:     GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCAT                         GGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA
genomic: GAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatg ... cctactccagGGTCTTTCGCTGGTCTAGGTTTTCTTGCATGGTACTTGGCTGGAAAACTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTTAATAATATAACCACCGATGTGATATGCCATGGAGAAAAGAGTGTCATCAAGGAAGGTCATAAGAGTTTCCCAAGTGGGCATTCTTCATgtaagaaatgaaattacttggtatataatgttcattatgcttcttgtggttatcttgatatgttatagtggtttattgttccactatcttgggatgtagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA