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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattgttgtatcatccttgtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC

Basic information

species Zea mays
transcript GRMZM5G833389_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 6
tcattgttgtatc-atccttgtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaac--attgttttgtgtgtg-acagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC
  ||||| |  |  ||  ||||   |    | |     | ||  |   |||| |||   ||  | | || |||||| | |||  |||| ||||| | |  ||||||||||||| || ||||||||||||||||||||||||||||| ||||| || ||||||||||||| ||||||||| ||||| || ||| | |||||||| 
--attgtggagtttatagttgtctattgtgcttatataaaataata--ttctgtcttagtccatttgtatttatgctgtaactcattgatttgtttttttacagTGAGACAGTGAAGTTTGGCCATGTCACATTTTTCTGGAACGGAAACCGATCTGGATACTTTGATGAAACTAAGGAAGAGTACGTTGAAATTCCTAGTGAT

upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 5
---tcattgttgtatcatccttgtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC
    ||   || | |   ||||  |    |  ||| |||||    ||  ||  |   |      |    || | |         |||  |||||     |||||||||| ||||||||||| || |||||||| |||||||| || ||||| || || || ||| || ||     |||||||||||| ||| | || ||||||
tttgcaacattttgtttaccttaagaactcttcattatctagtacttatctgttaaatgatggccatcatagtcacttgtatgaatttctttgt---caacagTGAGACTGTTAAATTTGGTCACGTCACATTCTTCTGGAATGGAAACCGCTCTGGGTATTTTAATTCAGAATTGGAGGAGTATGTGGAAATTCCCAGTGAC

upper sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 5
tcattgttgtatcatcctt-gtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC
      || | ||||  || ||| | |   | |  ||| || ||  ||   | |   |  |  ||||| ||  |  | |    || || | | | | |||||||||| || |||||||| ||||| || ||||||||||| || || || || || || |||||| ||| || |||||| ||||||||| | || ||||| 
gagggtttatttcatggttagtgataggttctttttcttcaattcaccagtttttaataccattctctgct-gtctaactctctttttctttctttaacagTGAGACTGTCAAATTTGGTCATGTTACCTTTTTCTGGAATGGAAATCGCTCAGGGTATTTTGATCCAAGTATGGAGGAATATGTAGAAATTCCCAGTGAT

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|61236681|gb|DN586426.1|DN586426
EST:     ATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCCCCCTTTTGCTTGCAG                         CGGAGACAGTTAAATTTGGCCCATGTCACATTTTTCTGGAACGGTAACC
genomic: ATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACC-TTT-GCTTGCAGgcaagtacta ... tgtgtgacagTG-AGACAGTTAAATTTGGCC-ATGTCACATTTTTCTGGAACGGTAACC
EST: gi|211244472|gb|FL127869.1|FL127869
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242245|gb|FL127865.1|FL127865
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242243|gb|FL127863.1|FL127863
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211240006|gb|FL127846.1|FL127846
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242246|gb|FL127866.1|FL127866
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211240010|gb|FL127850.1|FL127850
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242241|gb|FL127861.1|FL127861
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242239|gb|FL127859.1|FL127859
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211240009|gb|FL127849.1|FL127849
EST:     ATCTGGGGAGTACCTGGTGAAAGAATTGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ATCTGGGGAGTACTTGGTG-AAGAA-TGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242236|gb|FL127856.1|FL127856
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|33101669|gb|CF061629.1|CF061629
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211240007|gb|FL127847.1|FL127847
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242247|gb|FL127867.1|FL127867
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|26457193|gb|CA828776.1|CA828776
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACG
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACG
EST: gi|6637102|gb|AW261374.1|AW261374
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|6626545|gb|AW258077.1|AW258077
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242242|gb|FL127862.1|FL127862
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|67025128|gb|CO453877.1|CO453877
EST:     ACATCTGGGGAGTACTTGGTGAGGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|26456432|gb|CA828015.1|CA828015
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242238|gb|FL127858.1|FL127858
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
EST: gi|211242244|gb|FL127864.1|FL127864
EST:     ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAG                         TGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC
genomic: ACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTC

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), 20 (downstream exon)
Score: 24

AGTTGAAGCTTCCAAGCCGTTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC


Block sizes: 47 (upstream exon), 25 (downstream exon)
Score: 73

AGTTGAAGCTTCCAAGCCGTTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

AGTTGAAGCTTCCAAGCCGTTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

AGTTGAAGCTTCCAAGCCGTTACCTTGTTTCCCCACCAGAGATAGATAGAACATCTGGGGAGTACTTGGTGAAGAATGGCATCCGCACCTTTGCTTGCAGgcaagtacta ... tgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC
                                    attgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattgttgtatcatccttgtgcttgcaacatgatctacattttcccttctctctctctctctctctacttatgcagcaacattgttttgtgtgtgacagTGAGACAGTTAAATTTGGCCATGTCACATTTTTCTGGAACGGTAACCGTTCGGGATACTTTGATGCAACTAAGGAGGAGTATGTAGAAGTACCTAGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT