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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAA

Basic information

species Zea mays
transcript GRMZM2G009849_T01
intron # 34
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T03 (Zea mays), 3'ss of exon 33
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 51
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGT---CATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAA
                | ||   | |  |   |      ||||  |      || | | || | | |||| ||| |  || | ||| ||||| |  | |||||| || |||||||| ||||||||| |||||||||||||||||||||| ||| | |||    ||||||| |||| ||||||||| || ||| | || ||   
----------------gtctgccttctgtcatacttgctgttaagctgcacttctaagctt-tataatctgattgtatgaattgttctttctat-gccagCAGGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCAT---

upper sequence: GRMZM2G009849_T03 (Zea mays), 3'ss of exon 33
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTC---ATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAA
                | ||   | |  |   |      ||||  |      || | | || | | |||| ||| |  || | ||| ||||| |  | |||||| || |||||||| ||||||||| |||||||||||||||||||||| ||| | |||    ||||||| |||| ||||||||| || ||| | || |||||
----------------gtctgccttctgtcatacttgctgttaagctgcacttctaagctt-tataatctgattgtatgaattgttctttctat-gccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA
















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|71440205|gb|DR821255.1|DR821255
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCT---                         CAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|211104807|gb|FL044860.1|FL044860
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         --G-TACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|60347986|gb|DN214959.1|DN214959
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCT---                         CAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|76285312|gb|DV024880.1|DV024880
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCT---                         CAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|83278453|gb|DV942461.1|DV942461
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCT---                         CAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     AGGTCAAGGTGACGCCACTGACCAACANACTGATAGATACCAGACCTCAG                         --G-TACATTGGATGCTCTTTAGGAAAAGGATGAAA-GCATTCAAGCTGCA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTT-AGGGAAAGGATGAAAAGCATTCAAGCTGCA
EST: gi|60398867|gb|DN231683.1|DN231683
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCT---                         CAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|211409478|gb|FL448716.1|FL448716
EST:     AAACTGATAGATACCAG-CCT--T                         CAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
genomic: AAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     AGGTCAAGGTGACGCCACTGACCAACANACTGATAGATACCAGACCTCAG                         --G-TACATTGGATGCTCTTANGGAAAGGATGAANAGCATTCAAGCTGCAG
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... cttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAA
                                   ttcgttatttctttt  CT-rich tract
                        ttattattagattcgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagCAGGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA