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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
|||||| || || ||||||||||||||||| |||||||| ||||||||||| |||||||| || || |||||||||||||| || ||||||||| |||||||||| | | | |   | ||| |   | || |||||     | ||||||| | |   |              |||  ||     ||||  ||| |  |||  |||     ||| ||||
TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgat-tttgttccttaca---tttgcttggcatagtttttgcatt-tctaacattt-----------cttggtctggatttgaatgtggtgcccttattt-----aatttcag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
 || |||||||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || || |||||||| |||||||| |   |  | | |   ||   | || ||    || |   | ||   ||||||   | | ||    || |    ||  | ||     |  | || |  | |||| |  ||       
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatacat-gtgttcttcttgctagttgtgtcctgc-attttctttgtttatttccaaac-acctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcag------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
 || ||||||||||| |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||||||||| || || ||||| |||||||||||  |  |||| | |   ||       |||||||    | ||| |  | |   |     |  | |  | |  || |||   ||                                   
CCAGATATTTGAAGGCCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCTAGTGCATCTCTTGATCGGACAATAAAGgta-gaattatgttcttgtt------cctggttgtttcctatgatataatgcattaatgcacctgttgtcttctctttt-cag-----------------------------------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatc-ctattttttgtcaatatcag
 || ||||||||||| |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || || ||||| ||||||||||| |   |    ||   ||     ||  |  ||    | ||      |  | |    |  || |  | |      | | |||   ||    ||||    || || |       | ||||
CCAGATATTTGAAGGTCATTCTCATTATGTCATGCAAGTAACATTTAATCCCAAAGACACAAACACCTTTGCAAGTGCATCTCTTGATCGGACAATAAAGgtgtaattatgttcttgttcctggatgtttcttttttaaaaaaaaaaaaaagtaaaaa--gaaaaactatgatcctatgatataatg-cattgatgcaactgttatcatctcttttcag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgt-tatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttt--tgtcaatatcag
 || |||||||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||||||||||| ||||| || || |||||||| |||||||| | |   | | | |   |    | || ||      |   |  || | || |||  | ||      | |        | | |  || |  || || |  || | ||    |||||  |||
CCAGATATTTGAGGGACATTCTCATTATGTCATGCAAGTGACATTTAATCCTAAAGACACAAACACCTTTGCCAGTGCATCTCTTGATCGCACCATAAAGgtatatacatgtgttcttctcgctagttgtg-----tcctgaattttctttgtttatttccatacatctatga-----taaaaatttaaaagtaatgtattaatgttatcttcaattgcag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgt-ttgtgttatctccgctttaaaa----attctggtt--ggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| ||||| || || || || ||||||||||||||||| |||||||| |||||||| || ||||| ||||| ||||| ||||| ||||| || ||||||||  ||   |       | || |||    ||| |||||  | || |   ||    | |||        ||| ||     | | ||||                                      
TCAGATATTCGAGGGACACTCACACTATGTGATGCAAGTCACATTTAATCCAAAAGACACCAACACTTTTGCCAGTGCATCCCTTGATCGTACCATAAAGgtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcag-------------------------------------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| |||||||| || ||||| |||||||||||||||||   |||||| ||||||||||| ||||| ||||| |||||||| || ||||| || |||||||| |||   |  |||        |  | |  | |   |    |||  |  |   |||||    |    | ||  ||||| |||  | ||  | ||  | | ||  |  |||       
TCAGATATTTGAGGGACATTCGCACTATGTGATGCAAGTGGTATTTAATCCAAAAGATACCAACACTTTTGCCAGTGCTTCGCTTGATCGTACCATAAAGgtgtgtaagaggtccaagcactgagcttttatggctta----gtt--agcacgaggtactttta----aaagggttttcttagactaattttcatg-cttgttcatattcag------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggttggccacaatgttgcatta-tttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| || ||||| || || ||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||||||||| || ||||||||||| || ||||| ||   |   |   || |    |   || ||  |  || | ||  |  | ||| |   |  || |    ||  |  |  |       || |||||||   ||||             
TCAGATCTTTGAGGGCCACTCTCATTATGTGATGCAAGTGACATTTAATCCAAAAGATACCAACACTTTTGCTAGTGCATCTCTGGATCGCACCATTAAGgtatgatctggattttctgttggcaacttg-ttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccag---------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgttatctccgctttaaaaattctggt-tggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcag
||| || |||||||||||||||||||| ||||||||||| |||||||| |||||||| || ||||||||||| ||||| ||||| |||||||| |||||||| || ||         | |  | |  ||| | ||  |   | | ||  ||  |   |  |  |    |       || ||||| |||||  |  |     ||| | ||          
TCAGATTTTTGAAGGGCATTCTCACTACGTGATGCAAGTGACATTTAATCCAAAAGACACCAACACCTTTGCAAGTGCCTCCCTCGATCGCACTATAAAGgtgtgagtggaaatgtttcttgataacctgttgtgaacttgaagatgtgtt--tcaatgtc--ctaatgttgatccttccatag-ttgattttattg----attgtgtg----------

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 6
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 6
TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgt--------------ttgtgttatctccgctttaaaaattctggttggcc-acaatgttgca---ttatttggtaccgacaggcgacagcttt--ttcatagcttgatggtgatatcctattttt-tgtcaatatcag------------------------------------------------------
|||||| || |||||||| ||||| ||||| |||||||| || ||||| || ||||| |  ||||||||||| ||||||||  ||||||| ||  | |||||              ||  ||  | |    ||    | |  | | || |    ||| || ||   | ||  ||| ||    |   | ||||||    ||||          ||  | | | |  | |   | | ||                                                        
TCAAATTTTCGAAGGGCACTCTCATTATGTCATGCAAGTAACGTTTAATCCCAAAGACAGCAACACCTTTGCAAGTGCTTCTTTGGATCGAACTGTGAAGgtgaggtaccagttggttccgtcgtttatttttctgcagtattagctgtcttgaaatattacaaaatcatagggttccttatgctaatagctttaccccatattcaagcaacgaagttcaactgatgtaagattgtcttccaagacaatagaacaaaacgatggcttaattgtatggactgtctttttaacag

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|78107583|gb|DV526001.1|DV526001
EST:     CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAG                         ATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
genomic: CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
EST: gi|50325003|gb|CO520129.1|CO520129
EST:     CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAG                         ATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC
genomic: CAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCC

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: 174

TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 168

TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 110

TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

TCAAATATTTGAAGGGCATTCTCACTATGTGATGCAAGTTACATTTAACCCAAAAGATACAAACACCTTTGCTAGTGCTTCCCTGGATCGCACAATAAAGgtttgtgtta ... tcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC