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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagctttactttttttttttcagtatatcctgtcataggcagtgaaccatcgggaccctttgttgcttcttcgcaaagagatggttagcctaactttggtcgtttctaatggctaatgatgtttctgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCGTCCGATGCGGATGTCAAGGAAGCCGAGTCGCCCAAGGCCATCCAGAATA

Basic information

species Zea mays
transcript GRMZM2G147884_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 12
gtatcagctttactttttttttttcagtatatcctgtcataggcagtgaaccatcgggaccctttgtt--gcttcttcgcaaagagatggttagcctaactttggtcgtttc----taatggctaatgatgtttc------tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCGTCCGATGCGGATGTCAAGGAAGCCGAGTCGCCCAAGGCCATCCAGAATA
|||    | ||  ||||||||||  |  | |  |  ||    | ||     |||     | |||||     |  |||| | | |           ||   |||    || ||     || | ||  |  ||| |       | |  | ||||||||||| ||||||||||||||||| |||||||||||||||||| |||| ||||| || ||  |||||||||||||||||||||| |||||||||||  
gtaaagacctt-tttttttttttagaacaaagaccttctcttgtagcctttcatatctcctctttggcagacgacttctcta-gtttccaccgttctggtttttacagtatcagctcaaagcctgtttgtgtcttgtttaattcttttcagCCACATGGGTTCTTCAACTGCTCGCCGGCGGTCGACGTGCCTCCCGGCTCCTCCGACGCTGACATCAAGGAAGCCGAGTCGCCCAAAGCCATCCAGAACG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 11
gtatcagctttactttttttttttcagtatatcctgtcataggcagtgaaccatcgggaccctttgttgcttcttcgcaaagagatggttagcctaactttggtcgtttctaatggctaatgatgtttctgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCGTCCGATGCGGATGTCAAGGAAGCCGAGTCGCCCAAGGCCATCCAGAATA--
                                    |   | | |||||  |  | |   |     |||  |  | | | |    |   |     || |   ||  |  |  |  | |  ||||| || ||   ||||||||||||| |||||||||||||| |||||||| ||||| || || | | | |  ||   |||||  |||||    ||   |   | | | ||   | |    
------------------------------------ttgcatgtagtga--ctccagaggctcagtttgtctggtagaatatgcttccgtgcttgaaataatgtattgacccagtgtttttgatggttgtggg-tgcagCCACATGGGTTCTTCAACTGCTCACCTGCGGTGGACGTCCCCCCGAACGCTTGTGAATTGGATGGGAAGGACAATGA--TGTGAAGGACAATGGGGTAGCGA
















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|60342075|gb|DN209048.1|DN209048
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|211381837|gb|FL377365.1|FL377365
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|50326819|gb|CO521945.1|CO521945
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTNCA-CTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTC
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTT-CAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTC
EST: gi|86856190|gb|DY307201.1|DY307201
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|211487243|gb|FL369769.1|FL369769
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|50326828|gb|CO521954.1|CO521954
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|211542541|gb|FL409069.1|FL409069
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|67025362|gb|CO454111.1|CO454111
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAACTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|161590852|gb|EY958764.1|EY958764
EST:     CGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCC-AGCTCG
genomic: CGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|60397137|gb|DN229953.1|DN229953
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|60353904|gb|DN220877.1|DN220877
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|50326829|gb|CO521955.1|CO521955
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|88758266|gb|DY542407.1|DY542407
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|33942632|gb|CF349232.1|CF349232
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|4730397|gb|AI649563.1|AI649563
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|211466963|gb|FL423374.1|FL423374
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|60355304|gb|DN222277.1|DN222277
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|40337526|gb|CK371596.1|CK371596
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|21621426|gb|BQ619432.1|BQ619432
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|40334154|gb|CK368224.1|CK368224
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|113795973|gb|DW912970.1|DW912970
EST:     AGAAGATTGGCCNAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAAC
genomic: AGAAGATTGGCC-AGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAAC
EST: gi|78022408|gb|DV490795.1|DV490795
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|60339780|gb|DN206753.1|DN206753
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|88754474|gb|DY538615.1|DY538615
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|8102998|gb|AW927666.1|AW927666
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGTGGTCTACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|37400365|gb|CF637533.1|CF637533
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|60399063|gb|DN231878.1|DN231878
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
EST: gi|60355314|gb|DN222287.1|DN222287
EST:     TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATG                         CCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG
genomic: TAGAAGATTGGCCAGTCATGCCGGTGGAGCACATAGGCTTCATGCTCATGgtatcagctt ... tgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttagcctaactttggtcgtttctaatggctaatgatgtttctgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCGTCCGATGCGGATGTCAAGGAAGCCGAGTCGCCCAAGGCCATCCAGAATA
                                         tttctgccct  CT-rich tract
                      tttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcagctttactttttttttttcagtatatcctgtcataggcagtgaaccatcgggaccctttgttgcttcttcgcaaagagatggttagcctaactttggtcgtttctaatggctaatgatgtttctgccctgcagCCACATGGATTCTTCAACTGCTCGCCTGCGGTCGACGTGCCTCCCAGCTCGTCCGATGCGGATGTCAAGGAAGCCGAGTCGCCCAAGGCCATCCAGAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA