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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgctgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA

Basic information

species Zea mays
transcript GRMZM2G390076_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
gt-tgctgtgctctgaaagagtgtgacctacttattcc-cttataaagtgtatcaaccgtttactcatgtttttgccctgtta-aattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
||   |  |||||  ||  |   ||||||  |||||   ||||  ||||| ||  |    | | | ||  | ||||| ||||  ||||||||||||||||||||| || ||||| || |||| ||||||||| |||||||| || || |||||||| |||||||||||||||||||| |||||||||||||
gtgccccatgctcacaattacc-tgacctttttatttttcttaccaagtgaattgatttatcagttat--tcttgccttgttggaattcagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
--------------gttgctgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
              |    | || |  ||  | | |  |  ||  | |      |  | |  |||  |   |    |  | |||||| |||  |     |||||||| ||||||||||||||||| || ||||  || ||||| |||||||| |||||||| ||||| || ||||| |||||||| || |||||||| ||||
tttgtaccgtacatgcctttatgtttagatcgggggatag-taggtgtcaatcaactatgc-tattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G33040.1 (Glycine max), 3'ss of exon 2
--gttgctgtgctctgaaagagtgtgacc-tacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
   |    || || | ||| | |||||   || |   |       ||| |||| |||   | |  | || ||       |||||    |||||||| ||||| |||||||| || || |||| | | ||||| ||||| || || || || ||||| ||||||||||| ||||| || |||||||| ||||
gtttcatagtccttttaaata-tgtgattgtaatggctaggaatcaaaatgta-caatgttctgattatattgg----gtgtta----cagGTTGTAGAAGACGGATATGAATTCTTTGCTAACAGACAACTTGTAACTATCTTCTCGGCACCTAATTACTGTGGAGAGTTTGACAATGCTGGTGCTATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G41200.1 (Glycine max), 3'ss of exon 2
----------gttgctgtgctctgaaagagtgtgaccta--cttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
          |    | || |  ||  | | |  |      ||   ||   |||    |  |       ||   |  |||||| | ||| ||     |||||||| ||||||||||| ||||| || ||||  || ||||| |||||||| |||||||| ||||| || ||||| || ||||| || |||||||| ||||
tactgtacatgcctttatgtttagatcgggggatagtaggcctcgatcaactatgctattgaaagtaaattgttttttgttttcggcctttttttaccagGTTGTGGAAGATGGATACGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAGTTTGACAATGCTGGTGCTATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G00960.1 (Glycine max), 3'ss of exon 2
gttgc---tgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattc---agGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
||| |   ||   | |      |||     |   ||| |  || || |  |  |  |    |  |  |   || |    ||||   ||    ||||||| |||||||||||||||||||| || |   | ||||| || || || ||||| || ||||||||||||||||||||||| || ||||| || ||||
gtttcatatgcattttttttttgtgaagtttgagtatgcaattgtagaaagagttcaagtatagcataaacttcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAGTTTTTTGCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G00850.1 (Glycine max), 3'ss of exon 2
--gttgc-tgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
   ||   ||   |   |   ||| |||  |    | |   |   | |||  |   |  |  ||  | || || ||   | |    |  ||||||| |||||||||||||| |||||  | |   | ||||| || || || ||||| || ||||||||||||||||||||||| || ||||| || ||||
gttttatatgcatttctatgaagtttgag-tgtgcaattgttggaagagttcaagtattgcataacc-tgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
--gttgctgtgctctgaaagagtgtgacctacttattcccttataa-----agtgtatcaaccgtttactcatgtttttgccctgttaaatt------cagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
     | | ||     || |  |||||    |||||| | |  ||      ||    ||||   || |   | ||||||      | |||||      |||||||| || ||||| ||||| || || || | ||| ||||| ||||| || ||||| || ||||| || ||||| || |||||||| |||||||||||||
cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaatt-ttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA

upper sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0049g00890.t01 (Vitis vinifera), 3'ss of exon 2
---gttgctgtgctctgaaagagtgtgacctacttat--tcccttataaagtgtatcaaccgtttactcatgttt----ttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
      ||| || | |       ||     |  || |  || | | ||||         |  ||| ||| |  |     || || ||||   | |||||||| ||||||||||| |||||||| ||||   | ||||| ||||| || |||||||| ||||| |||||||| || |||||||| || ||||||||||
gtttcagctctgttttagctttttgcattttttttttggtcacctttaaacctctcaggcatttttctcttactacatatttccttgtt--gtgcagGTTGTGGAAGATGGATACGAGTTTTTTGCTAATAGACAACTTGTAACCATATTTTCAGCACCTAATTACTGTGGTGAGTTTGATAATGCGGGTGCCATGA

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|6695722|gb|AW288800.1|AW288800
EST:     CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAG                         GGTGGCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
genomic: CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
EST: gi|69351419|gb|DR452128.1|DR452128
EST:     CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAG                         GTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
genomic: CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
EST: gi|93284121|gb|EB676385.1|EB676385
EST:     CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAG                         GTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
genomic: CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
EST: gi|60359288|gb|DN226261.1|DN226261
EST:     CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAG                         GTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
genomic: CTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG
EST: gi|113840975|gb|DW966372.1|DW966372
EST:     GATTTGGACCTCATCTGCCGAGCCCATCAG                         GTTGTCGAAGATGGATATGAGTTTT-CGCTAGCCGCCAACTCGTAACAATG
genomic: GATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATG

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: 47 (upstream exon), 49 (downstream exon)
Score: 140

GGCCATAAATGATCGAGGTGTTTCATATACATTTGGTCCTGATAAAGTTTCTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA


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

GGCCATAAATGATCGAGGTGTTTCATATACATTTGGTCCTGATAAAGTTTCTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GGCCATAAATGATCGAGGTGTTTCATATACATTTGGTCCTGATAAAGTTTCTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 87

GGCCATAAATGATCGAGGTGTTTCATATACATTTGGTCCTGATAAAGTTTCTGAATTCCTTGAGAAGCATGATTTGGACCTCATCTGCCGAGCCCATCAGgttgctgtgc ... ttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
                                        ccctgtt  CT-rich tract
     ttataaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA