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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATATGCTGATGGAAGCATCTGTTTGGATATCCTACAGAACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgcactttgttgagcagattttttagtgcaaaaatggatgtttagtgataatggctaactcacttaagagttttatcaacatcaacatagcctt...

Basic information

species Zea mays
transcript GRMZM2G074479_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074479_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 4
TATATGCTGATGGAAGCATCTGTTTGGATATCCTACAGAACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgcactttgttgagcagattttttagtgcaaaaatggatgtttagtg--ataatggctaactcac-ttaagagttttatcaacatcaacatagcctt----
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TTTATGCAGATGGAAGCATCTGCTTGGATATTCTACAGAACCAGTGGAGCCCTATATATGATGTTGCTGCCATATTGACTTCAATTCAGgtaccttt-------ttgatcaattttcagactagcaaaaagcatttgtaatgccatgaagagtagtgcttaccatgagtaatgagatctttctaggtgcattattt
















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|211442711|gb|FL002353.1|FL002353
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|113562978|gb|DW737678.1|DW737678
EST:     TGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: TGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|1298473|gb|W21709.1|W21709
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|31558421|gb|CD527633.1|CD527633
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|76913363|gb|DV165094.1|DV165094
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|60352657|gb|DN219630.1|DN219630
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|18170555|gb|BM340395.1|BM340395
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|6031234|gb|AW076136.1|AW076136
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|71759581|gb|DR957518.1|DR957518
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|5650301|gb|AI920661.1|AI920661
EST:     AGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGGGTGATCCAAACCCAAACTCCCCTGCAA-CTCAGAAGCAGCA
genomic: AGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|5871231|gb|AW017702.1|AW017702
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|5871291|gb|AW017762.1|AW017762
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|5871290|gb|AW017761.1|AW017761
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|18383724|gb|BM416924.1|BM416924
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
EST: gi|18649199|gb|BM498033.1|BM498033
EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAG                         TCCCTGCTGGGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgca ... gtttttgcagTCCCTGCTGTGTGATCCAAACCCAAACTCCCCTGCAAACTCAGAAGCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATATGCTGATGGAAGCATCTGTTTGGATATCCTACAGAACCAGTGGAGTCCTATATATGATGTTGCTGCAATTTTAACTTCTATCCAGgtaccttgcactttgttgagcagattttttagtgcaaaaatggatgtttagtgataatggctaactcacttaagagttttatcaacatcaacatagcctt

- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC