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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaagttatagctcaaatgtttagagaaattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgttt...

Basic information

species Zea mays
transcript GRMZM2G121942_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 4
AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaagttatagctcaaatgtttagagaaattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgttt----
 || || ||||| || ||||||||||||||||||||||| ||||||||| ||||||||||||| ||||| || |||||||| ||||||||||| ||||||||||    |  |  ||| || |||  | |       | | |    |||| |   |     |  |||| ||||| |  || |   |  ||||  |     |    
GGATAGCTATGCATCCTATATTGGGCACTATCCAATGCTGGCATATTTTTCCATTGCTGAGAATGAATCAATTGGAAGAGAGCGTTACAATTTTATGCAGgtatg--ttaaaagcttattataacatgtcttctgtacggtagttgaaaattatgt-tggacttatc-tggtttattaatattgatgtagaactgctcctaaaa

upper sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaagt-tatagctcaaatgtttagagaaattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgttt
 || |||||||| || || ||||| ||||| || |||||  |||| ||||| |||||||||||||| || || ||| ||||||| ||||||||||||||||| ||||||||  || | |  |  |  |||  ||        |    ||  |  ||  ||  | |   ||  | |    |    || ||       ||  |
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgt-ttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt

upper sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 5'ss of exon 3
AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaa-gttatagctcaaatgtttagaga-aattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgttt
 || |||||||| || || ||||| ||||| || |||||  | || ||||| || |||||||||||||| || ||  ||||||||||||| ||||||||||| |     | |   |||||||    | ||  |    |    ||  || |||  ||  |  | | | || |     | |  |||  ||||||  || | |  
TGATAGTTATGCTTCATACATTGGTCACTACCCGATGCTTTCTTACTTTGCAATAGCTGAGAACGAATCTATTGGTCGAGAACGTTACAACTTCATGCAGgtttgtttactatctttcttcttgcatcatgtcaaggaatcatattgagaatgttaatgtgttagtgtcttaagggagaggaac--aattagggttgtttca

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|19057527|gb|BM736194.1|BM736194
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|45847222|gb|CN071165.1|CN071165
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCCCTGTGGCCTTGCCTCCCGAGAGAGATGAAGATTGAA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCT-TGTGGCCTT-CCTCCCGAGAGAGATGAAGATTGAA
EST: gi|211191929|gb|FL276017.1|FL276017
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|78111599|gb|DV529996.1|DV529996
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|19057691|gb|BM736358.1|BM736358
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|18163701|gb|BM333540.1|BM333540
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|19436871|gb|BM953281.1|BM953281
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCCCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|101402755|gb|EB822903.1|EB822903
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|5714327|gb|AI944312.1|AI944312
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|149110102|gb|EE293919.2|EE293919
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|5108428|gb|AI740141.1|AI740141
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|32864255|gb|CF003937.1|CF003937
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|18171587|gb|BM341427.1|BM341427
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|113794906|gb|DW910687.1|DW910687
EST:     TCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: TCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|149076642|gb|EE165281.2|EE165281
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|32943241|gb|CF048060.1|CF048060
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|211088951|gb|FL225884.1|FL225884
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|60350040|gb|DN217013.1|DN217013
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|211191924|gb|FL276012.1|FL276012
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|211194321|gb|FL276023.1|FL276023
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|32937147|gb|CF041966.1|CF041966
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
EST: gi|56462064|gb|CK986362.1|CK986362
EST:     CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAG                         AAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA
genomic: CCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctc ... ctttgtacagAAAATGCTGCTTCCTTGTGGCCTTCCTCCCGAGAGAGATGAAGATTGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaagttatagctcaaatgtttagagaaattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaaa