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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctcctagaccaccagtacatgtatttattttcttgaaatgattgaaatcatgacatttactaatgccactaaaaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG

Basic information

species Zea mays
transcript GRMZM2G165535_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 8
gtgagtctcctagaccaccagtacatgtatttattttcttgaaatgattgaaatcatgacatttactaatg--ccactaaaaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG
          ||  ||  |  | |   ||   || | |  ||||| ||||   |||||| |||||||  ||   ||||  ||     ||||| || || ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||
---------gtaagccttctatcctcatacaaatgtgccagaaattattggtttcatgatatttactgctgtatcactttaa-----cagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGACAAAACCTACAAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g58580.2 (Oryza sativa), 3'ss of exon 8
gtgagtctcctagaccaccagtacatgtatttattttcttgaaatgattgaaatcatgacatttactaatgc--cactaaaaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG----------
          ||  ||  |  | |   ||   || | |  ||||| ||||   |||||| |||||||  ||   ||||  ||     ||||| || || ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||          
---------gtaagccttctatcctcatacaaatgtgccagaaattattggtttcatgatatttactgctgtatcactttaa-----cagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGACAAAACCTACAAGGTGATATGTA

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 9
-gtgagtctcctagaccaccagtacatgtatttatttt--cttgaaatgattgaaatcatgacatttactaatgccactaaaaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG
 || |||         ||  |    ||||  | |||||   ||  |   | ||| |     |||  | |||||   | || |      ||||| || || ||||||||||||||||| || ||| ||||||||||||| |  ||  | ||||| || ||||| || || || || ||||| 
tgtaagtaatgattttcatgacatgatgtggtgattttatttttgataaagtgatagttcaacaggtcctaatttaaatatact-ccacaGGTTTTCCCTCAAGGTTGGGACAAAACATACTGCCTGAGATATCTTGATGGTTTCAATGAAATTCACTTCTTCGGTGACAAAACTTACAA-

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 9
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtctcctagaccaccagtacatgtatttattttcttgaaatgattgaaatcatgac---atttactaatgccactaaaaaattc--cagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG
|||||| |||     || |  ||  | |  ||   |  ||  ||   | | |   |||||   || || |  ||    |||    |    ||||| || |||||||| |||||||| || || ||||||||||| ||||| || ||||  |||||||| |||||||| ||||| || ||| ||
gtgagtgtcc--attcatctttatttttgctttgatgattcgaaaactagtatcaatgactgaatgtattgctggtcataatgcttgtgacagGTTTTCCCCCAAGGCTGGGACAAGACATACTGCTTGAGATACCTTGATGATTTTCCTGAAATCCACTTCTTTGGCGATAAAACATACGAG

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|6020771|gb|AW065579.1|AW065579
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|5871671|gb|AW018142.1|AW018142
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|85151824|gb|DW587525.1|DW587525
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTGTTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|76011520|gb|DT938690.1|DT938690
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|5361143|gb|AI795758.1|AI795758
EST:     CGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGCCAAAACTTATTGCTTGAGATATTTTGAGGAA
genomic: CGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|71449147|gb|DR830197.1|DR830197
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTG
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTG
EST: gi|211038831|gb|FL468651.1|FL468651
EST:     TGCACACCATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TGCACA-CATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|45846830|gb|CN070773.1|CN070773
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|32919709|gb|CF024521.1|CF024521
EST:     GGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: GGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|14700950|gb|BI233368.1|BI233368
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|5871104|gb|AW017545.1|AW017545
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|6056459|gb|AW090849.1|AW090849
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGC
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGC
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|40302745|gb|CK347132.1|CK347132
EST:     GGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: GGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|32909183|gb|CF013995.1|CF013995
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
EST: gi|32909184|gb|CF013996.1|CF013996
EST:     TTGCACACATGAACTTGACATTTTCTATCGGTGNGTAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttgaaatgattgaaatcatgacatttactaatgccactaaaaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG
                                        actaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctcctagaccaccagtacatgtatttattttcttgaaatgattgaaatcatgacatttactaatgccactaaaaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG

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