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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttttctgaaggctaaatgatatggatttgctgtattggactacctctgattactattatttttctgcag

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 7
GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttttctgaaggctaaatgatatggatttgctgtattggactacctctgattactattatttttct-gcag
||||||||||| ||||||||  |||||||||| ||||||||||| || ||||| |||||||||||||| |||||||| |||||||| ||||||||||||    ||    ||  ||   |  || | ||||          || ||||||||| |  | || ||  | ||||||  |||
GTTGCATGTGCTTTGCTGCTATCTGGTGAGAATTTGGATAACTTCGGTGATGTTAAGAACATTCTTGTGGAAATGGGGACATACTTCCAAGTTCAGgtaccttttcaccttgttggttgtgaatttatatat--------tactggactaccgc--actaatacgagttttctcacag

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 8
GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttt---tctgaa-----ggct--------aaatgatatggatt------tgctgtattgga--ctacctctgattactattatttttctgcag--------
|||||||||||||||||  |||| |||||| |  | || ||   ||  |||||||||||||||||||| || |||||||||||||||||||| |||||||| ||||  | |   | |||      ||||        | || || | || |      |||||||||  |  ||| || |  |  || |  |||| |             
GTTGCATGTGCATTGCTTATGGCGGGTGAGGATCTAGACAAAAATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAGgtaatactttgttataggtttgacctcttggctttctttagagatcatttagactctagaatgctgtattataacctatcttttttctctttccttttcccctctcattttag

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G34770.1 (Glycine max), 5'ss of exon 1
----------GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttt---tctgaa-----ggct--------aaatgatatggatt-tgctgtattggactacctctgattactattatttttctgcag----------------------------------------------------
          ||  ||| |||||||||  |||  |||||| |  | || ||   ||  |||||||||||||||||||| || |||||||||||||||||||| ||| |||| ||||  | |   | |||      ||||        | || || | ||   |    | ||| |   |     ||| |  ||||     || |                                                     
CCTTACACAGGTGACATATGCATTGCTTATGGTGGGTGAGGATCTAGACAAAAATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAgtacagataatactttgttataggtttgacctcttggctttctttagagatcatttagaccctagaatgttgtatgtctatatattgcccttatgagcttgaaatattttattataacctatcttttttctctttccttttcccctctcattttag

upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 8
GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttttctgaaggctaaatgatatggatttgct---gtattggactacctct-gattactat-tatttttctgcag----------------------------------------------------------------------------------
|||||||||||||||||  |||| |||||| |  | || |||  ||  |||||||||||||||||||| || |||||||||||||||||||| |||||||| |||| ||| |    ||| |  |     ||| |||  |     ||     |  |||| || | || | | | | ||| ||                                                                                   
GTTGCATGTGCATTGCTCATGGCGGGTGAGGATCTTGACAACCATGTTGATGTAAAGAACATTCTTGTTGAGATGGGAACATACTTTCAAGTACAGgtaatacttt-gttat----aggtttgacctcttggctttctttagagatccttttgactctagaatgctgtctgtatgtctacatattgccctcatcagctataaatattttttaaaaactgtattataacctatcttttctctatccttttcccctctcattttag

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|148986684|gb|EE030466.2|EE030466
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|60355786|gb|DN222759.1|DN222759
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|148995918|gb|EE035161.2|EE035161
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|148972760|gb|EE023733.2|EE023733
EST:     TAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: TAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|6194630|gb|AW146734.1|AW146734
EST:     GCGATGGAAAGAACATTCTTGGCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|211433629|gb|FL480968.1|FL480968
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTAAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCCAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCCTTGGCAAGAT
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAGAT
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     CGATGTAAAGA-CATTCTTGTCGAAATGGGAACATACTTTTCAAGT-CAG                         GATGATTATT-AGATTGTTTCGGTGATCCTGAATTC
genomic: CGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTT-CAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTC
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAAT
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAAT
EST: gi|148943252|gb|EC888313.2|EC888313
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATCCCTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
EST: gi|111189546|gb|EE287682.1|EE287682
EST:     GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAG                         GATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG
genomic: GCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG

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: 45 (upstream exon), 43 (downstream exon)
Score: 38

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 37

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 21

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 99

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttt ... ttttctgcagGATGATTATTTAGATTGTTTCGGTGATCCTGAATTCATTGGCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGATAACTTTGGCGATGTAAAGAACATTCTTGTCGAAATGGGAACATACTTTCAAGTTCAGgtaatgcttttgttttctgaaggctaaatgatatggatttgctgtattggactacctctgattactattatttttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC