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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcactgcatgcatgcgcttcttcctgcactatactccttattatattattgcctaatcggaaaataataataatttccatttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG

Basic information

species Zea mays
transcript GRMZM2G138268_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------gtgagc--actgcatgcatgcgcttcttcctgcactat-actccttattatattattgcctaatcggaaaataataataatttcc----atttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
                                                        | | |  | |  | | |   |  |    ||    ||| | ||| |  | |     ||  |  | | |   | |  ||  | |      ||   | |||||||||||| || |||||||||||||||||| |||| ||||||||||||||||| |||||||| |
gtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagtccatgctctgcatctgtgttct-gaattctgaccattttgtttggaaatggaaatttcagGATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTG

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g43400.1 (Oryza sativa), 3'ss of exon 3
-gtgagcactgcatgcatgcgcttcttcctgcacta-tactccttattat--attattgcctaatcggaaaataataataattt-ccatttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
 |||   | |   |  |  ||           | || | ||| | ||  |  ||  |   ||  |||  || |  |  |      |      |  | ||||||||||||||| || ||||| ||||| || ||||||||||| || |||||||||||||| |
ggtgtcaaatattttgaaacggagggagtaataataattctcttgatctttaatcctcatctcgtcgttaattgtttgttgcaaactgacatacgtgcagGATGTTCGTCGAGTCGTGCAAACGCCTCCGAATCATGAAAGGGTCTGAAGCCATTGGCCTTG

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G36790.1 (Glycine max), 3'ss of exon 2
gtgagcactgcatgcatgcgcttcttcctgcactatactccttattatattattgcctaatcggaaaataataataatttccatttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
         |   |    |  |  ||| | || | | ||  |  || | | |||  | |       |||| ||    |||        ||  |||||||||||| |||||||||||||| ||||| || |||||||| || || || || || || |
---------gtcagtgccccttcattcattcatt-tccttttctttctttaattatcaacctatttaatactacctttttttgacaatttcacagGATGTTCGTTGAATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G32340.1 (Glycine max), 3'ss of exon 3
--gtgagcactgcatgcatgcgcttcttcctgcactatactccttattatattattgcctaatcggaaaataataataattt-ccatttcattttc---agGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
  |  |    |  |   ||       ||  |      ||     |||| || |  ||   |  |   |||| | | |||||  |  ||| ||||||   |||||||| || |  |||||||||||||| || || ||||| ||||||||||| |||||||| |
cagaaacttatatacttatatagccattaattagtcttatagtatattttaattctgtaaatccatgaaatta-attaattaactgtttaattttctgaagGATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G40760.1 (Glycine max), 3'ss of exon 2
gtgagcactgcatgcatgcgcttctt--cctgcactatactccttattat----attattgcctaatcggaaaataataataatttccatttcatttt-cagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
|| ||  ||| |    |     |||   |   ||| | |  | | |||||    |  ||| |   ||   | | || ||||  |    || | ||||  ||| |||||||| ||||||||||||||||| || || ||||||||||| || || || || || |
gtaagt-ctggaccattatttctctaagcacacaccacatccttaattattaggaccatttctcgattaaacattactaatt-tggatatataatttcacagAATGTTCGTGGAATCATGCAAGCGCCTGCGTATAATGAAAGGATCTGAGGCAATCGGGCTAG

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0081g00010.t01 (Vitis vinifera), 3'ss of exon 3
gtgagc-actgcatgcatgcgcttcttcctgcactatactccttattatatt---attgcctaatcggaaaataataataatt--tccatttc----attt---tcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
|| ||  ||  |||     |  |  || |     || | |  ||   |   |   ||    |||||   | ||  || |||||  ||| | |     ||||   ||||||||||||||||||| ||||||||| | || || ||||||||||| || ||||| || || |
gtaagttacaacatttg-acaatattttccaatttaaattgtttcaaaggcttacatcaattaatccatagattttactaattaatccttctttggaatttgaatcagGATGTTCGTCGAATCTTGCAAGCGCTTGCGCATAATGAAAGGATCCGAGGCCATCGGACTTG

upper sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g04690.t01 (Vitis vinifera), 3'ss of exon 3
------gtgagcactgcatgcatgcgcttc-ttcctgcactatactcctta-ttatattattgcctaatcggaaaataataataatttccatttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
       ||   |     |  ||| |     |||   ||  | ||     | ||  |  |    ||| |    |||   |||    ||  |||||||   ||||||||| || || |||||||||||| | || || ||||||||||||||||| ||||| || |
ttgtagttggttatcatctatatgggtaaaattctcacatgaaacaataaaattccaccaaaagcta-tgactaaagtttaagctgtttgatttcatg--cagGATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG

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|32829750|gb|CD969428.1|CD969428
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGACGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|32929462|gb|CF034274.1|CF034274
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGACGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|78180728|gb|DV551101.1|DV551101
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|32829307|gb|CD968985.1|CD968985
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGACGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|32829634|gb|CD969312.1|CD969312
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGACGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCG-CTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|32830201|gb|CD969879.1|CD969879
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGACGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|44901509|gb|CK828054.1|CK828054
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|88753298|gb|DY537439.1|DY537439
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
EST: gi|4681090|gb|AI629760.1|AI629760
EST:     TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGA                         GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC
genomic: TACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGC

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: 177

ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagcactg ... tcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattatattattgcctaatcggaaaataataataatttccatttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG
              gcctaat  putative branch site (score: 105)
                                     tttccatttcattttc  putative PPT
                        aaaataataataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcactgcatgcatgcgcttcttcctgcactatactccttattatattattgcctaatcggaaaataataataatttccatttcattttcagGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC