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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgggtttcggattatgtggaaatggaaaataggaagatgtagccccatgcttgtatccccctggttgacaattttttttcatggttttattcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG

Basic information

species Zea mays
transcript GRMZM2G161566_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161566_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 1
cgggtttcggattatgtggaaatggaaaatagga--agatgtagccc-catgcttgtatccccctggttgacaattttttttcatggttttattcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
    ||   ||| | |   |    ||||||   |  || |||        |  |   |     | |    |       |  || |  | || ||||||| ||||||||||||  ||||||||||| ||||| ||||| ||| || | |||
---cttctagatcaagccaatcctgaaaattccacgaggtgtgatttatgtcttcacaaatttcagacaaattgacgctcctcgttatattgttcctgtgcagGTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG
















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|89251386|gb|DY623172.1|DY623172
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAA-CTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|71320315|gb|DR796905.1|DR796905
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211098206|gb|FL312089.1|FL312089
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|148935612|gb|EC879655.2|EC879655
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|74244986|gb|DT652900.1|DT652900
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211424454|gb|FL316412.1|FL316412
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211307748|gb|FL198215.1|FL198215
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|30087806|gb|CB886012.1|CB886012
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCTTTTN                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|148962769|gb|EE013680.2|EE013680
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211306681|gb|FL364492.1|FL364492
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211494300|gb|FL310097.1|FL310097
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211213913|gb|FL360058.1|FL360058
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGA-                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211537841|gb|FL338654.1|FL338654
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211274785|gb|FL366576.1|FL366576
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACNAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211307749|gb|FL198216.1|FL198216
EST:     TCGCGGGTCCAADCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         -TCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|101387955|gb|EB815991.1|EB815991
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|31664615|gb|CD573548.1|CD573548
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|78078108|gb|DV506523.1|DV506523
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211105937|gb|FL329403.1|FL329403
EST:     TCGCGGGTCCAAGCCCGTCGTATCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211151343|gb|FL367847.1|FL367847
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211101919|gb|FL367365.1|FL367365
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|71447774|gb|DR828824.1|DR828824
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211265503|gb|FL351831.1|FL351831
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|91048521|gb|EB158939.1|EB158939
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|78116794|gb|DV535181.1|DV535181
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|71447773|gb|DR828823.1|DR828823
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAAAAATCATCCGGAG                         GTCATGAAAATTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211168848|gb|FL341411.1|FL341411
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211485657|gb|FL310062.1|FL310062
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGAGA
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAGAGA
EST: gi|211491457|gb|FL310570.1|FL310570
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|88757481|gb|DY541622.1|DY541622
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211104289|gb|FL362968.1|FL362968
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         -TCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
EST: gi|211477893|gb|FL342552.1|FL342552
EST:     TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAG                         GTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
genomic: TCGCGGGTCCAAGCCCGTCGTACCGCTCCGTGCGAAGAAATCATCCGGAGgtattttttt ... tcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcttgtatccccctggttgacaattttttttcatggttttattcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG
                 ggttgac  putative branch site (score: 4)
                                       ttttattcct  putative PPT
                        aattttttttcatggt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgggtttcggattatgtggaaatggaaaataggaagatgtagccccatgcttgtatccccctggttgacaattttttttcatggttttattcctgtacagGTCATGAAAACTTGCATAACTCCGTTGACGAAGCTCTCCTGTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG