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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagtgcgggcttgcggcagtcaacccctggcgacaatttgatttaagctgtgtagttttgcaacagtttcttttcagtagcattcaagattatttttctcagtgcagtgcacgatagtaaaaatatataaaaaaagaaggcttgtattcttgtattattcacaaaggagctatttttcag

Basic information

species Zea mays
transcript GRMZM2G014069_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 12
GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagtgcgggcttgcggcagtcaacccctggcgacaatttgatttaagctgtgtagttttgcaacagtttcttttca-gtagcattcaagattatt-tttctcagtgcagtgcacgatagtaaaaatatataaaaaaagaaggcttgtatt--cttgtattattcacaaaggagctatttttcag
||||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||||||||||||| ||          |||  | | || | |  |||  |||  || |  ||     ||||   ||     ||||  |||||  |  || ||  | ||  || || ||||   |  |||  | |||   ||| ||| |    |  || | |||| ||   | || || || |||| |    ||||||||||
GAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAGgtattgtg--------ttgtagtactctagcattggttacacattaacctataaaatgtaacattctgctagttctttttcctgcggcctttcaaatggttcttcctcatgacgctgccagctaggggaaagata-accgcagcaaagattgttttggttggtgttgtttacaatgtgaatatttttcag

upper sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA13G27810.1 (Glycine max), 5'ss of exon 12
GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagtgcgggcttgcggcagtcaacccctggcgacaatttgatttaagctgtgta---gttttgcaacagtttcttttcagtagcattcaagattatttttctcagtgcagtgcacgatagtaaaaatatataaaaaaagaaggcttgtattcttgtattattcacaaaggagctatttttcag
||    ||  |  |||| ||||| |||||||| ||||| |||||||||||||| || || || ||||| ||||||||||||||   | | | |   ||      | |   |  ||| | | |||  |||| ||       |    | ||| |  |  |  || || |||  ||    ||| |  |                                                                                     
GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAGgt---gaattacatactctaattattttgctactg-ctataataagattaaaaaaaaagatgcatcttgtatgaactg-ttatctgtaatatattggatcaaata------------------------------------------------------------------------------------

upper sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT3G23940.2 (Arabidopsis thaliana), 5'ss of exon 12
GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagtgcgggcttgcggcagtcaacccctggcgacaatttgatttaagctgtgtagttttgcaacagtttcttttcagtagcattcaagattatttttctcagtgcagtgcacgatagtaaaaatatataaaaaaagaaggcttgtattcttgtattattcacaaaggagctatttttcag
|| || ||  | ||||| |||||||| || ||||| |||||||| || |||||||| || ||||| ||||||||||| ||||| ||      |   |||       ||   | ||| | ||    ||  |  | | | | |   ||  ||       ||| || | |||    |||| | |||  |   | ||   |                                                                      
GAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAGgt-ctctctctctcccttttttttttc--tctctgcccac----tggctccatcagagcaaaattctaaa-----ttttgcacttgca----agataaatttgatagatccatgtc----------------------------------------------------------------------

upper sequence: GRMZM2G014069_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 5'ss of exon 12
GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagtgcgggcttgcggcagtcaacccctggcgacaatttgatttaagctgtgtagttttgcaacagtttcttttcagtagcattcaagattatttttctcagtgcagtgcacgatagtaaaaatatataaaaaaagaaggcttgtattcttgtattattcacaaaggagctatttttcag
||    ||  || |||| |||||||| ||||| ||||| |||||||||| |||||| || |||||||| ||||||||||| ||||            ||       ||    |||       ||    ||| |  | | || ||||   |          |||| | |    |||||||| ||              |  | || | ||||| | || | || ||                                          
GATGTTGCTTTGTTGACTGATGGTAGGTTTTCAGGAGGTTCACATGGATATGTTGTTGGCCACATATGTCCTGAAGCACATgtac----------attt-------tcttttcct-----tcatccagttttatttttttatttttttga----------tcagaaacgaagaagattatatta-------------ataaaagaacaaatacagaagagaaaaaa-----------------------------------------

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|211042827|gb|FL411666.1|FL411666
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|149101994|gb|EE188015.2|EE188015
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|71311152|gb|DR791882.1|DR791882
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|9953481|gb|BE640064.1|BE640064
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|33095072|gb|CF055066.1|CF055066
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGATCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|211152609|gb|FL453070.1|FL453070
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCMCCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|5688808|gb|AI941823.1|AI941823
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCCCATATGCCCTGAAGCCCAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|45568073|gb|CK985888.1|CK985888
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|74234928|gb|DT642842.1|DT642842
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|5895787|gb|AW037033.1|AW037033
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
EST: gi|211085449|gb|FL413518.1|FL413518
EST:     CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG                         GAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT
genomic: CTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGAT

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), 47 (downstream exon)
Score: 105

GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGATGTAAGTAAGAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 60

GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGATGTAAGTAAGAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAG


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

GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGATGTAAGTAAGAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagt ... tatttttcagGAAGGTGGTCCAATTGGCCTTGTCCAGAGTGGTGATATAATCACCATCGATGTAAGTAAGAGGGTAATCGATGTTGACCTTACCGAACAGCAGCTCGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAGgtactgcagtgcgggcttgcggcagtcaacccctggcgacaatttgatttaagctgtgtagttttgcaacagtttcttttcagtagcattcaagattatttttctcagtgcagtgcacgatagtaaaaatatataaaaaaagaaggcttgtattcttgtattattcacaaaggagctatttttcag

- - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC