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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactgaaaaaactgctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA

Basic information

species Zea mays
transcript GRMZM2G094390_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 3'ss of exon 2
atcctttggaaagtttaacatagttcac-taacatttttactttatgcagttgcacactgaatgacttaatcaatactgaaaaaactgctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA
   ||   |||  |  |   ||    |  ||| |  ||    ||  |  || ||   ||   |  ||  |       |||    |||||| |||| ||||||||||||||||||||||| ||||| ||||||||| ||||||||||||| ||||| || || |||||||| ||||||||||| ||||||||||||||||||
-gactacagaatttacatgctaaacaatataagaacttcttgtttagttgtggccttcttttttgctggaaacccgttgagttgactgctgcaatctgcagGTCAACAAATTTGGATTCGTGGACCCCAGAACAATTGAAAATGATGGTTTATGGAGGTAACAACCGTGCACAAGCTTTCTTCAAGCAGCATGGTTGGACA

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
-atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactgaaaaaactgcta--caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA
 || || || ||      | ||     |   |     ||  |  ||  |   | |||   ||||| || ||   ||   ||| |  ||||   | ||||| ||||| |||||||| || ||||||| ||| || ||||| ||||  |||  || ||| ||||| || ||||| || | |||||||||||| ||||||||||  
tattctgtgaaacacactatattcagaatgtaggaagttgttgaatagaaa-gaacag-aaatga-ttgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 3
atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactgaaaaaactg------ctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA
        ||||     |||   |   |  | | |   |  || |  | | | |    ||   |    ||  |||   ||| ||||       || | ||||| ||||| |||||||| || ||||||| ||| || ||||| |||| ||||  || ||| ||||| || ||||| || | |||||||||||| ||||||||||| 
------atgaaacaaacacactatattcagaaagtaggaagttgttgaatagaaagaagacaaaaaagattgataggtaaataactatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACGATGAGCTTTGGAGGAAACAATCGTGCACATGGTTTCTTTAAGCAACATGGTTGGACT

upper sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactga---aaaaactgctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA
||   | |   | ||     |  | |  |  | |||||  || |  |  ||  | | |   ||  ||| | | | |||    ||||| || |    |   |||||| |||||||| || ||||||| | |||| ||  | || ||||||  || ||| ||||| |||||||| || |||||||||||||||||||| ||| | 
atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttt-tgttttactaattgctgtgccaaaaattgatttgct--ccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT

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|211011501|gb|FL284249.1|FL284249
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211008716|gb|FL284228.1|FL284228
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211011498|gb|FL284246.1|FL284246
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211005952|gb|FL284225.1|FL284225
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211005945|gb|FL284218.1|FL284218
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211008725|gb|FL284237.1|FL284237
EST:     GACTGCTCGGCGGNGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211008727|gb|FL284239.1|FL284239
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|89755431|gb|DY685850.1|DY685850
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|93282709|gb|EB674973.1|EB674973
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|101394873|gb|EB819371.1|EB819371
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACACATTTGGATTCATGGACTCCAGAACAACCTGAAAATGATGGTCT
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAAC-TGAAAATGATGGTCT
EST: gi|6578063|gb|AW244200.1|AW244200
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211005949|gb|FL284222.1|FL284222
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|50326040|gb|CO521166.1|CO521166
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211011496|gb|FL284244.1|FL284244
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|91868839|gb|EB400177.1|EB400177
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211011493|gb|FL284241.1|FL284241
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211005951|gb|FL284224.1|FL284224
EST:     GACTGCTCGGCGGCGCACCS-AGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
EST: gi|211008718|gb|FL284230.1|FL284230
EST:     GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGG
genomic: GACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGG
EST: gi|31350258|gb|CD434615.1|CD434615
EST:     ACTGCTCTGTC-CCGCAACGCAGCCTCGGCGTCCACGTCTCCTTCGTCAG                         GTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA
genomic: ACTGCTC-GGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTA

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: 46 (upstream exon), 49 (downstream exon)
Score: 22

CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 80

CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 52

CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 50

CCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCGTCCACGTCTCCTTCGTCAGgtcgcctcgc ... caatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagttgcacactgaatgacttaatcaatactgaaaaaactgctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA
                  acttaat  putative branch site (score: 50)
                    ttaatcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactgaaaaaactgctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - -gcagttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa