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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtccttatatatatcggggaaaaaatgttgtgcaatcaagctttccgtgcaatcgccgccaatcaaattatcaaaagtcatgatattttttta...

Basic information

species Zea mays
transcript GRMZM2G137615_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137615_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 17
TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtccttatat-atatcggggaaaaaatgttgtgcaatcaagctttccgtgcaatcgccgccaatcaaattatcaaaag-tcatgatattttttta-----
||||||||||||||||||||| ||||||||||| ||| | || |||||||| ||||||||||| ||  |||||||   |||||||||||| || ||||||||||| ||||||| | | |||      |  || |  | |  ||| |     ||       || ||    |||||| | | ||||  |  |  ||  || | |     
TCTTTTGGAGCATTACAATGGTAAATGGCCCTTGTGGTTGAGTCCTCGCCAAGCCATTGTTTGCTCCATATCTTCCAATTCAGTGGAATACGCTAAACAGgtaaaaggtccttgtgtcatagaatttactaattactat-taattagtagctct------tctccattgatcaaagtgtgaaaatcttctagtaccttctgattcga

upper sequence: GRMZM2G137615_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtccttatatatatcggggaaaa---aatgttgtgcaatcaagctttccgtgcaatcgccgccaatcaaattatcaaaagtc-atgatattttttta
 ||||||||||| ||||| || ||||||||||| ||||| || || || ||||| ||||||||  | || ||       ||   |  ||||||     |||||  |   |  |||  | ||   | ||       |  |||  |    |  ||    |   || ||   |  | || ||     || || ||| |  |      
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgctcactctaaactttctggaaatctatgctgatgc----
















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|32933232|gb|CF038044.1|CF038044
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|211198162|gb|FL344190.1|FL344190
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|5791229|gb|AI978021.1|AI978021
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|211313757|gb|FL309500.1|FL309500
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCT
EST: gi|60337159|gb|DN204132.1|DN204132
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|26559875|gb|CA832110.1|CA832110
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|211513903|gb|FL285080.1|FL285080
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|87156412|gb|DY401201.1|DY401201
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAA
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAA
EST: gi|30052636|gb|AI065926.2|AI065926
EST:     AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: AGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
EST: gi|71770369|gb|DR968306.1|DR968306
EST:     GCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAG                         GTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT
genomic: GCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGT

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: 48 (upstream exon), 48 (downstream exon)
Score: 190

TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 183

TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtc ... ctgataccagGTTCTTGCCATGCTACATGAAGCTGATTTCCATGTTGATATTGATGTGAGTGACAGGACAATACAAAAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtccttatatatatcggggaaaaaatgttgtgcaatcaagctttccgtgcaatcgccgccaatcaaattatcaaaagtcatgatattttttta

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgccgcc