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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctgtcctagtttttagcttcttagctaacgtgtacactgccctgttccag

Basic information

species Zea mays
transcript GRMZM2G108087_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g47440.1 (Oryza sativa), 5'ss of exon 5
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctgtcctagtttttagcttcttagctaacgtgtacactgccctgttccag
||||||||||| ||||||||||| ||||| ||||||||||||||||||||||  || || ||||||||||| |||||||||   |||||| | | ||||||||||| ||||||||| | ||| |||||  |||  |  |  |  ||||| ||| ||||  |||||      | || |||
AGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagt-tttacattgcactgtacatatcatgtgttgttcctgtgcttcctagttaacacgtacatc-ttttattacag

upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g47440.2 (Oryza sativa), 5'ss of exon 5
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctgtcctagtttttagcttcttagctaacgtgtacactgccctgttccag--
    ||||||| ||||||||||| ||||| ||||||||||||||||||||||  || || ||||||||||| |||||||||   |||||| | | ||||||||||| ||||||||| | ||| |||||  |||  |  |  |  ||||| ||| ||||  |||||      | || |||  
----AGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGGCAAgt-tttacattgcactgtacatatcatgtgttgttcctgtgcttcctagttaacacgtacatc-ttttattacagag

upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G01960.1 (Glycine max), 5'ss of exon 5
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaa----gtctttacattgt--attgtgcatatgctgtcctagtttttagcttcttagctaacgtgtacactgccctgttccag---------------------------------
|| ||||||| ||||||||| |||||   |||||||||||||||| ||||  | |||||||||||||||   ||||| |||   ||||||   || || || ||    || ||| |  |     || |||  ||      |    || ||   | ||    || || || |||    | ||  |                                  
AGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAAGTAAATGAGATTTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCAATGATTGgtaacttagtttttcccctcccagttttgctaattacacacattcttgtactatatttttaaatgtctagacttttttttttaattttaaactttgatgtaaaatttccattttgtag

upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 5
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctg--tcctagtttttagcttcttagctaacgtgtacactgccctgttccag-------------------------------------
|||||||||| ||||||||| || |||||||| |||||||||||  ||||  | |||||||||||||||   ||||| |||   ||||||  ||| || || || |  || ||||   || ||    | |||  | || |  | |    | |||   || |  |  | |   |||| || |                                     
AGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTGCTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccatttccttttgttcttcctgattacttgcatctt-tattttactgaatgaatttatttttctgtacctgttcacgctatctaatgccactaaatttcattttgtag

upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G13410.1 (Glycine max), 5'ss of exon 5
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctg--tcctagt-ttttagcttcttagctaacgtgtacactgccctgttccag-----------------
|||||||||| ||||||||| || || ||||| |||||||||||  ||||  | |||||||||||||||   ||||| |||   ||||||  ||| || || || |  || ||||   || ||    | |||  | || || | ||   ||    |     |   ||| | ||  || |||                  
AGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAAGTTAATGAGATCTTCAAAGATCTTGCTGTACTTGTCCATGAGCAAGGAGCCATGATTGgtaatttattccattcccttttgttcttcctggttacttgtatctttattttactgtacctgctcacattacctagtgccactaaatttcattttgtag

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|76286077|gb|DV025645.1|DV025645
EST:     AGTGGTCAAAGATCTTGCTACCCTTGTGCATTCCCCAGGAATCATAATCG                         AGGAAATCGACATGAACATTGAAAA
genomic: AGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATTGAAAA
EST: gi|78117098|gb|DV535485.1|DV535485
EST:     AGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCG                         AGGAAATCGACATGAACATTNGAAAT-TCTGCAGCAGTGACCAAAGAGGCA
genomic: AGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATT-GAAAAATAAGCAGCAGTGACCAAAGAGGCA
EST: gi|78074309|gb|DV502743.1|DV502743
EST:     GTGTTCAAAGATCTTGCTACCCTTGTGCATTTCCCAAGGA-TCATAATCG                         AGGAAATCGACATGAACATTTGAAA
genomic: GTGTTCAAAGATCTTGCTACCCTTGTGCATT-CCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATT-GAAA
EST: gi|71768040|gb|DR965977.1|DR965977
EST:     GTGTTTCAA-GATCTTGCTACCCTTGTGCATTTCTA-GGAATCATAATCG                         AGGAAATCGACATGAACATTTGAAAT-TCTGCAGCAGTGACCAA
genomic: GTGTT-CAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATT-GAAAAATAAGCAGCAGTGACCAA

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: 67

AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATTGAAAAATAAGCAGCAGTGACCAAAGAGGCAAAGACACACCTAGCTTTAAAAAGGCACGACTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATTGAAAAATAAGCAGCAGTGACCAAAGAGGCAAAGACACACCTAGCTTTAAAAAGGCACGACTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATTGAAAAATAAGCAGCAGTGACCAAAGAGGCAAAGACACACCTAGCTTTAAAAAGGCACGACTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtcttt ... cctgttccagAGGAAATCGACATGAACATTGAAAAATAAGCAGCAGTGACCAAAGAGGCAAAGACACACCTAGCTTTAAAAAGGCACGACTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAAGTACATGAAGTGTTCAAAGATCTTGCTACCCTTGTGCATTCCCAAGGAATCATAATCGgcaagtctttacattgtattgtgcatatgctgtcctagtttttagcttcttagctaacgtgtacactgccctgttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA