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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtaggcctgtctctaacaaacacctgtaggg...

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 3
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtaggcctgtctctaacaaacacctgtaggg-------
|||||| |||||||||||||||||||||||||||  |||||||||||||||  ||||||||||||| || ||||||||||| ||||||||||||||||||||||||   |  |       |  |||||||      ||   |  |   |     ||    |    |  || |    |||     | ||| |  | | |||       
ATCATTCGGGTCTGCACTTGAATTTGTTTGGTCAGTTGATGGAGAATATGCTGTCAGAGAAAGCACGTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgtactaccac------tgtcccttcttttaattatctttgtacatcagagtaggggtccttcaatgcaa-tgtgtgggctagaaaaatttattgggtgtgcac

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 12
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtag-gcctgtctctaacaaacacctgtaggg----
|||||| |||||||||||||||||||||||||||  |||||||||||| ||  |||||||||||||||| ||||||||||| ||||||||||||||||||||||||       |  |   | ||||||||      ||   |  |   |     ||    |    |  || |  |  ||   |||  |||     |||||     
ATCATTCGGGTCTGCACTTGAATTTGTTTGGTCACTTGATGGAGAATACGCTGTCAGAGAAAGCACCTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgtac-----tgcccactgccccttcttttaattatcgttgtacatcagagtaggggtccttcaatgcaatgtgtggggctagaaaaatttagtaggtgtgc

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtaggcctgtctctaacaaacacctgtaggg----
 |||||||| || ||||| ||||||||||||||  |||| |||||||||||  |||||||||| || |||| ||| || |||| ||| ||||||||||||||||||     | ||| |  ||    | ||| ||  |    ||   | ||  ||| | | | ||  |    |   |    |||  | |   | |  | ||    
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatctt--gttctgtgtgtaatgaaccaa--caagttcttgctatttcttaaaaggaaaa

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 12
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtaggcctgtctctaacaaacacctgtaggg----
 |||||||| || ||||| ||||||||||||||  |||| |||||||||||  |||||||||| || |||| ||| || |||| ||| ||||||||||||||||||     | |   |  |||   | ||| ||  |    ||| |  | | ||| | | | ||  |    |   |    |||  | |   | |  | ||    
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttttaaacttcatttcctctctaatct--tgtgtgatcttgttctttgtgtaatgaaccaa--caagttcttgctatttcttaaaaggaaaa

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 16
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgt--ttcaatataacatattccccttctccctggta-----caatgttttgtttagttatatct-ataccgctgtaggcctgtctctaacaaacacctgtaggg---------------
 |||||||| ||||| || ||||||||||||||| ||||||| ||  ||||  |||| |||||| |  ||| ||| ||||| | ||| || |||||||||||||||  |||  | |  ||  ||||  |||   ||| |       || | |||  ||  || | ||| || | | | |  |     | |||||  |  |   ||                  
GTCATTTGGCTCTGCGCTAGAATTTGTTTGGTCATCTGATGGGGAGCATGCTGTCAGGGAAAGCTCGACAAAGATCAAGATCTTCAGCAAGAATTTCCAGgtttgtaattccttttggcacgttccttttccgactgattaactctaaagcttttgttttttgtgtcttattctgttatctgaaatacactaacctatgctgatacccttgtttaatttgcag

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 12
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtt----tcaatataacat-----attccccttctccctggtacaatgttttgtttagttatatct---atacc-gctgtaggcctgtctctaacaaacac-ctgtaggg--------------------
||| ||||||||||  || ||||||||||||||| |||| || |||| |||  | ||||||||| | |||| ||||||||| | ||||||||||||||||||||| |    ||| |||  | |     || |   ||       |||  ||  |  | ||    | ||     || |  ||  |||      || | ||   |    | ||                       
ATCTTTTGGGTCTGGCCTGGAATTTGTTTGGTCATCTGAGGGGGAATGTGCGGTTAGAGAAAGCTCATCAAAGATAAAGATATTCAGTAAAAATTTCCAGgtttgctattctcattatggccttactcatactattttgttggagtatgattctagggttgaagaaattgcagatgcttgcaatagagacagctattactggcttattatattaataaaaggtggtgttttcag

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggt-acaat-gttttgtttagttatatctataccgctgtaggcctgtctcta-acaaacacctgtaggg---
 || ||||| || ||| | |||||||| |||||| | ||||| ||||||||  |||||||||| || |||| | | ||||||| |||||| ||||||||||||||| ||       | |  |    ||||| ||| | | ||| | || | |    ||||| ||||    || | |  ||| | |       |  ||| |      
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcc------cctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt

upper sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 12
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttg-----tttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtaggcctgtctctaacaaacacctgtaggg
||||||||| || || || ||||||||||||||| | |||| |||||||||  | || ||||| || |||||||| ||||||| ||| ||||  ||||||||||      ||||||  |      |  | |  ||   || |      |||| |  |   | ||    |  |||       |||  | ||        | |    
ATCATTTGGCTCAGCGCTGGAATTTGTTTGGTCATCAGATGCAGAATATGCTGTGAGGGAAAGTACATCAAGGATTAAGATTTTCAGCAAAACATTCCAGgttttgatcctttcaaagtttagattctcacgacttattgatgggggcttttctccaagcaaattagcaatgcttc--ttttgttgcaaagttgtttatctt---

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|31355222|gb|CD439579.1|CD439579
EST:     CCATCAGAGAAAGCACCTCAAGGATAAAGATTTATAGTAAAAATTTCCAG                         GAGAGGAAAAGTATAAGACCATCATTTTCGGTTGAACGGATATTTGGTGGT
genomic: CCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttca ... gtctttccagGAGAGGAAAAGTATAAGACCATCATTTTCGGTTGAACGGATATTTGGTGGT




















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: 172

ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttca ... gtctttccagGAGAGGAAAAGTATAAGACCATCATTTTCGGTTGAACGGATATTTGGTGGTGTGTTACTTGCTATGTGTACAAATGACTTCATTTGCTTTTATGATTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttca ... gtctttccagGAGAGGAAAAGTATAAGACCATCATTTTCGGTTGAACGGATATTTGGTGGTGTGTTACTTGCTATGTGTACAAATGACTTCATTTGCTTTTATGATTGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 175

ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttca ... gtctttccagGAGAGGAAAAGTATAAGACCATCATTTTCGGTTGAACGGATATTTGGTGGTGTGTTACTTGCTATGTGTACAAATGACTTCATTTGCTTTTATGATTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 208

ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttca ... gtctttccagGAGAGGAAAAGTATAAGACCATCATTTTCGGTTGAACGGATATTTGGTGGTGTGTTACTTGCTATGTGTACAAATGACTTCATTTGCTTTTATGATTGGG