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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_T05
intron # 9
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|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|148950412|gb|EC895979.2|EC895979
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCTCA-GGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGA
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCC-CAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGA
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCCAAGGT-GGGACAAAACTTATTGCTT
genomic: TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCC-AAGGTTGGGACAAAACTTATTGCTT
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|76280415|gb|DV019983.1|DV019983
EST:     TTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT                         GTATTTCCCCAAGGTTTGGACAAAACTTATTGCTTGAGATATCTTGAGGAA
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 93

GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 202

GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 148

GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 161

GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcc ... aaaattccagGTATTTCCCCAAGGTTGGGACAAAACTTATTGCTTGAGATATCTTGAGGAATTTCAAGAAATCCATTTCTTTGGGGATAAGACCTACAAG




 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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA