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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtatagtttctttagctcggcgctgcacatcatgtgagtagtaccttccaccatgcgcatttactctgctgtctatctgctgctggtttccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG

Basic information

species Zea mays
transcript GRMZM2G520535_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G520535_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 6
--ggta-tagtttctttagctcggcgctgcacatcatgtgagtagtaccttccaccatgcgcatt---tactctgctgtctatctgctgctggtttccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG
   | | |       ||  ||  ||  |||| ||    |||||  |||||||||  |||  ||||   || || ||||| ||    ||| |||||  | | | |||| ||||||||||||||||||||||| ||||||||||| ||||| || |||||||| ||||||||||||||| ||||||| |||||||| || || |||||
ttagcactcagcatgttgtcttagccgtgcatat---atgagttataccttccattatgatcattatttaatcagctgttta---actgttggttctcctcttcagTAAAACCGGTAAAGGGTGATGCCCTTCTGTTCTTCAGTCTCCACCCCGATGCAACAACAGACTCTGACAGCCTGCACGGGAGCTGCCCGGTCATTGAAGG

upper sequence: GRMZM2G520535_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0066g02170.t01 (Vitis vinifera), 3'ss of exon 7
ggtatagtttctttagctcggcgctgcacatcatgtgagtagtacctt-ccaccatgcgcatttactctgctgtctatc-tgctgctggtttcct---tgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG
     |   |||| |  ||   |  || ||   | |  ||  |       | || ||    |    |     |||| |  ||   |   ||| ||     |||||| || ||    || ||||||||| ||||||||||||| || |||||||||||||| |||||| |   |||||| || || || ||||| || || |  ||
-----atactcttcatttcattgtcgcccaagttttttgtgatttaaggtctccctgtatttcattttcagagtctgttatggctcacatttgctgtacttgcagTGAACCCCAAGAAAGGTGATGCCTTGCTGTTCTTCAGTCTGCATCCTGATGCAACCACAGACCCAAGCAGCTTACATGGAAGTTGCCCTGTTATTGCGGG
















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|74236044|gb|DT643958.1|DT643958
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|71442479|gb|DR823529.1|DR823529
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|60355536|gb|DN222509.1|DN222509
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCACCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|211251396|gb|FL479077.1|FL479077
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|211039974|gb|FL073405.1|FL073405
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATG
EST: gi|149014492|gb|EE044118.2|EE044118
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|71320428|gb|DR796958.1|DR796958
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCTATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|148951226|gb|EC896920.2|EC896920
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|76019346|gb|DT946516.1|DT946516
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|60399600|gb|DN232411.1|DN232411
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|211387056|gb|FL031625.1|FL031625
EST:     CTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: CTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|24767600|gb|CA402744.1|CA402744
EST:     CTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCACCCTGATG
genomic: CTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|71328190|gb|DR800733.1|DR800733
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|71442480|gb|DR823530.1|DR823530
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|31353117|gb|CD437474.1|CD437474
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCACCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|78180250|gb|DV550623.1|DV550623
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCACCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|76287083|gb|DV026651.1|DV026651
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|71320427|gb|DR796957.1|DR796957
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|32866418|gb|CF006100.1|CF006100
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATG
EST: gi|74236045|gb|DT643959.1|DT643959
EST:     ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG                         TTAAACCCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGAT
genomic: ACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACC-GGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGAT

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), 49 (downstream exon)
Score: 194

GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 130

GGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAGgtatatagca ... ccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccaccatgcgcatttactctgctgtctatctgctgctggtttccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG
                                          tttccttgt  CT-rich tract
              atttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatagtttctttagctcggcgctgcacatcatgtgagtagtaccttccaccatgcgcatttactctgctgtctatctgctgctggtttccttgtgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGCCTCCATCCTGATGCAACGACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGTAATCGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - gctgcac
- - - - - - - - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctg