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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtttccttgagagtcgtatgtttacactttatattaatctggctatccttctttagccttttgttatccactataagctttaatttcattttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAGATGGAGAAGCTACTGCAAGACCAAGAAGCCATGAGGACCACTCTTCTTC

Basic information

species Zea mays
transcript GRMZM2G128995_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128995_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------------------------gtaaggtttccttgagagtcg---tatgtttacactttatattaatctggctatccttctttagccttttgttatccactataagctttaatttcattttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAGATGGAGAAGCTACTGCAAGACCAAGAAGCCATGAGGACCACTCTTCTTC
                                                                           || |  ||||     | | |    |    | || | | | ||  |||| |        | | ||  ||   | ||  | || | |||  ||| | ||  | | ||||| || ||||||||||| ||| ||||||||||||||||| ||||| | ||| |||| |||||| |||||||||| ||||| |||||| |  | ||||| |
gtaaatttgccgtcctaactttttcatcaaaaacctttgtttacacttcacatttagcttttatccctagagccttaggagttccaaataacttgggacagaaattcagtct-tgtttttctgtccccatcaatctggcaattctctgtcacccattaacttgtattacgttgaaatacagGTTCGCGATTTTGAGTATAGTTCTGAAGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGC
















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|67019107|gb|CO447856.1|CO447856
EST:     GACAATTTTTAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: GACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|148963814|gb|EE014911.2|EE014911
EST:     CAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|32907249|gb|CF012062.1|CF012062
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|40334835|gb|CK368905.1|CK368905
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|60338283|gb|DN205256.1|DN205256
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|71427970|gb|DR809020.1|DR809020
EST:     CTAAGGTTGTTGACAATTTTAAGGTCTGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAG
EST: gi|148954149|gb|EC899548.2|EC899548
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTT
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTT
EST: gi|37401333|gb|CF638029.1|CF638029
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|32910284|gb|CF015096.1|CF015096
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|60354564|gb|DN221537.1|DN221537
EST:     CAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|12972189|gb|BG267858.1|BG267858
EST:     TGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: TGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|60358961|gb|DN225934.1|DN225934
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|67032136|gb|CO460885.1|CO460885
EST:     AAGGNTGNTGACAATTTTAANGGTCCGTGCTCGCGAGAAAGGGTTT-CAN                         N
genomic: AAGGTTGTTGACAATTTTAA-GGTCCGTGCTCGCGAGAA-GGGTTTTCAGgtaaggtttc ... tttattccag-
EST: gi|67032136|gb|CO460885.1|CO460885
EST:     AAGGNTGNTGACAATTTTAANGGTCCGTGCTCGCGAGAAAGGGTTT-CAN                         N
genomic: AAGGTTGTTGACAATTTTAA-GGTCCGTGCTCGCGAGAA-GGGTTTTCAGgtaaggtttc ... tttattccag-
EST: gi|149000733|gb|EE037951.2|EE037951
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|149098810|gb|EE184821.2|EE184821
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|148968977|gb|EE019671.2|EE019671
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|148968978|gb|EE019672.2|EE019672
EST:     TAAGGTTGTTGANCA-TTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAG
genomic: TAAGGTTGTTGA-CAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAG
EST: gi|40303110|gb|CK347497.1|CK347497
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|149000703|gb|EE037917.2|EE037917
EST:     GTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: GTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|67017448|gb|CO446197.1|CO446197
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|149010225|gb|EE042044.2|EE042044
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCA
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCA
EST: gi|149000734|gb|EE037952.2|EE037952
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCT
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCT
EST: gi|149098811|gb|EE184822.2|EE184822
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCG
EST: gi|148963815|gb|EE014912.2|EE014912
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGA
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGA
EST: gi|78076481|gb|DV504915.1|DV504915
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|211201056|gb|FL359983.1|FL359983
EST:     AATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: AATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|67013699|gb|CO442448.1|CO442448
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|37378328|gb|CF625849.1|CF625849
EST:     GAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: GAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
EST: gi|71427969|gb|DR809019.1|DR809019
EST:     CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAG                         GTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG
genomic: CTAAGGTTGTTGACAATTTTAAGGTCCGTGCTCGCGAGAAGGGTTTTCAGgtaaggtttc ... tttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccttctttagccttttgttatccactataagctttaatttcattttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAGATGGAGAAGCTACTGCAAGACCAAGAAGCCATGAGGACCACTCTTCTTC
                                 ctttaat  putative branch site (score: 4)
                                       tttcattttattcc  CT-rich tract
                           tataagctttaatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtttccttgagagtcgtatgtttacactttatattaatctggctatccttctttagccttttgttatccactataagctttaatttcattttattccagGTCCGTGATTTTGAGTACAGTCCTGAAGCACAGGAAAGTCGGAAGCAGGAGATGGAGAAGCTACTGCAAGACCAAGAAGCCATGAGGACCACTCTTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC