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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtggtttctgtttgaacattagcgtaacttcatatctgctagtggccataaccacatgacttttccttccttttgctccag

Basic information

species Zea mays
transcript GRMZM2G079538_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 6
AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtggt-------------ttctgtttgaacattagcgtaacttcatatctgctagtgg-ccataaccacatgacttttccttccttttgctccag
||||||| |||||||| ||||||||||| || ||||| |||||||||||||||||||||  |    |             |||||| |||| |     | || ||   |        | | |  | |  |  |  | || |||| || |   |||||
AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgt-attccag

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 5'ss of exon 3
AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtg---gtttctgtttgaacattagcgtaacttcatatctgctagtggccataaccacatgacttttccttccttttgctccag
||||||| || |||||| ||||||||||  |||| || || |||||||||||||||||||   |     ||| |  ||   ||||    |||   ||| | || ||      | || |   |   |  | | |  || ||    ||
AACCTGGTGAGAGAGTCCAGGCTGATGAGGCTATTGCACAAATTGAAACTGATAAGgtatcaatatttattttttctttgtcatttttctaaagacatctgtgttaaattttaaaatctattatttgattcatatttgtggattag
















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|148950981|gb|EC896624.2|EC896624
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|211169879|gb|FL077608.1|FL077608
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGT
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGT
EST: gi|211325989|gb|FL407943.1|FL407943
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|148943959|gb|EC889039.2|EC889039
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|31355469|gb|CD439826.1|CD439826
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|31355590|gb|CD439947.1|CD439947
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|149015063|gb|EE044815.2|EE044815
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|5343075|gb|AI795485.1|AI795485
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|78103875|gb|DV522298.1|DV522298
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|148958216|gb|EC904424.2|EC904424
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|148991485|gb|EE033000.2|EE033000
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|149081048|gb|EE170148.2|EE170148
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|211169872|gb|FL077601.1|FL077601
EST:     AGACAGAGTCGANGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTT
genomic: AGACAGAGTCGA-GGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTT
EST: gi|148931436|gb|EC874404.2|EC874404
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|31358640|gb|CD442997.1|CD442997
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|148978727|gb|EE026283.2|EE026283
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|149014456|gb|EE044070.2|EE044070
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|32808216|gb|CD960450.1|CD960450
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|149003557|gb|EE038930.2|EE038930
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|211321201|gb|FL380429.1|FL380429
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATANATGTCNCAAGTCCTGAGGCTGGTGTTATTGAAAAGCTCATT
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGCTCATT
EST: gi|7145229|gb|AW506710.1|AW506710
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|31353408|gb|CD437765.1|CD437765
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|211169881|gb|FL077610.1|FL077610
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTG-AGGCTGGTGTTATTGAAAAG
EST: gi|67033243|gb|CO461992.1|CO461992
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG
EST: gi|29576970|gb|CB617082.1|CB617082
EST:     GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAG                         GTCACTATAGATGTCGCAAGTCCTGAGGCTGGAGTTATTGAAAAG
genomic: GAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtgg ... tttgctccagGTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtggtttctgtttgaacattagcgtaacttcatatctgctagtggccataaccacatgacttttccttccttttgctccag

- - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - -  GCAGAT