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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT

Basic information

species Zea mays
transcript GRMZM2G054136_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 4
gtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
||| | || ||   | | ||   |  ||| || |    || |  | | ||   ||| | |  |  ||  | ||    |   | ||| || || ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||
gtaaaaaggctctatttctattattgactttcgga--tat-tcatgcccttgctctgaccatattat--gttacttgtatggcagGCACACCTTGCTTCCGTGGGTATGGCAGGCGTGATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTCAGCCAGGACCTATCTGTTATTAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 4
------gtatagagacttcctatt------tacagtgtactctcagcaccatcttttactctgattcttatctgaa----cattcgatatcaattc-tgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
      |||  |    ||  |||         |||   ||| | |||  || | |||  | |  ||   || | ||    |||| | |    |  | || ||| ||||| || |||||||||||||| ||||| ||||| ||||| |||||||||||||| ||||| ||||| || ||||  ||||| |||||| |||||||
tttgaggtactgtttttttttataactggactcaggaaacttttagc--caacctttgttattttttcaatgttaaatttcatttgttgcttacccatgcagGAACTCCTTGTTTCCGTGGTTATGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G31840.3 (Glycine max), 3'ss of exon 3
---gtatagagacttcctatttacagtgta----ctctca--gcaccatcttttactctgattcttatctgaacattcgatat------caattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
    |  |  || ||     ||  | |  |     | |||  |||  ||  |   |  || || ||  | ||    |  || |      || ||  | ||| ||||| || |||||||| ||||| ||||| ||||| ||||| || ||||||||||| ||||||||||| || || | ||| || |||||| | ||| |
tttatgcaatgatttttagctttaactagaaaccttttcattgcaggattctcagccatgtttatttgcagacttgttaatgttttttgcatttgagcagGAACTCCTTGTTTCCGTGGATATGGAAGGCGCAATGGAGAGCGTAGAAGGAAGTCTGTTCGTGGTTGCATTGTCAGTCCAGATCTCTCTGTTTTGAACCT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 4
----------------gtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                || ||  |  ||  |  ||| | |    | ||  ||   ||||||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
ttattaatttttaatagtgtaatgcatttgttgttata-tcaggtgtctacattttcttttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAGCGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G31130.1 (Glycine max), 3'ss of exon 5
-------gtatagagacttcctattta--cagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatat------caattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
         ||  | | ||  | ||||   | ||   | |||  ||||  || |  | |   ||  || | ||  |||  | |       |  |  | ||| ||||| || ||||||||||| || ||||| ||||| ||||| |||||||||||||| ||||| ||||| || ||||  ||||| |||||| |||||||
agtaaggtcatgtatatttgttttttaggtactgctttttcataaccaatttatgttattggtccaatgttaaatttctgtttgttgcttacctgagcagGAACTCCTTGTTTCCGTGGTTACGGAAGGCGCAATGGAGAGCGTAGGAGGAAGTCTGTTCGTGGGTGCATTGTCAGCCCTGACCTCTCTGTTCTCAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 3
-----------gtatagagacttcctatttacagtgtac----tctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
            | ||   |  || |   |    ||||     | ||    |  || |||      |  || || |     ||   | | | ||    ||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || |||| |||||| |||||| | |||||
ctttattcattttttaataatgtcatgcatttgttgtatcaggtgtctctgctttcctttgtctacaaactaattttctttttatttgttacttgaacagGAACTCCTTGCTTCCGTGGATATGGAAGGCGTAATGGAGAACGTAGGAGAAAGTCTGTTCGTGGGTGCATTGTCAGCCCAGACCTCTCTGTTTTGAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 4
gta-tagagact-tcctatttacagtgtactctcagcaccatcttttactctgattct------tatctgaacattcgatatcaattctgt----agGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
||| ||||  |   || ||| | |   |  |       |  | |||| |  | ||  |      | | |    ||  ||| |   |  |||    ||| ||||| || ||  | ||  | || ||| | | ||| ||| | ||  | |||||||||||||||||||| |||||||  ||||| |||||| | |||||
gtactagattccaccccattgataaaattatacagcttctctttttttcattaatcttctgtgttttttatttatgtgatctggttattgtgtttagGTACTCCTTGTTTTAGAGGACACGGAAGGAGGACTGGAGAGAGGAGACGAAAGTCTGTCCGTGGTTGCATTGTGAGCCCTGACCTGTCTGTTCTTAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------------gtatagagactt---cctatttacagtgtactc--tcagcaccatcttttactc---tgattcttatctgaac--attcga-------tatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                                                                                  | | |  | ||   ||| ||  || |||  |   |  |   |||  |  | |     ||| |||     |||  || |||       | |   ||    ||| || || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||| ||||| || ||| | |||||
gttggtagactggtctactactttgtgcatatttagatgtgaaacaattaaatgcagtttttatatattgttttggagtttatttgggcattttctcctgttagcattgtggttaatttgtctcattctgcatttgctcgatgcttgatgaaactaatacgaattggcattttgcttgaacagGCACCCCTTGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGATGCATTGTTAGCCAGGACCTCTCAGTTTTGAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtatagagacttcctatttacagtgtactctcagcaccat-cttttactctgatt---cttatctga------acattcgatatcaattct-gtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                 ||    |  |||   |  |       || || |    |||  |||||  |   ||     |||  ||      ||| |  ||    |||   | ||| || || ||||||||||| ||||| || |||||||| ||||| ||||||||| |||| ||||| ||||| || ||||||||||| |||||| | |||||
gtgagtaaactgggactgttctaatccttaaaaactgatcacaacccttaagttcatatttttatgcaagttgggtctatgagatttattacactttatgcttatttgagcagGTACCCCATGCTTCCGTGGATATGGAAGACGTAATGGAGAGCGAAGGAGGAAGGCTGTTCGTGGGTGCATTGTCAGCCAAGACCTCTCTGTTTTGAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------gtatagag-acttcctatttacagtgtactct--cagcaccatcttttact--ctgattct------tatctgaacatt----cgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                                                           || ||  ||  ||  ||   ||  |  | |   || ||||| ||||  |  ||  |  |      |   |||| | |       | |   ||  | ||| || || ||||| || || ||||| ||||||||||| ||| | ||||||||| |||| ||||| ||||| || ||||| ||||| |||||| | |||||
gtgggtttttggtggtatattagtgttggtgcactgaccaccattccttcaagtttaagatggatcacggccagttagaagcatgttttgctaggaccatgttttgttgccttgtcatagatgatggatgaaaactgttctagttttgcttaagcagGAACCCCTTGCTTTCGAGGATATGGTAGGCGTAATGGAGAGAGGAGGAGGAAGGCTGTACGTGGGTGCATTGTCAGCCAGGACCTTTCTGTTCTGAACTT

upper sequence: GRMZM2G054136_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 3
gtatagagacttcctatttacagtgtactctcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                      ||  |         |  | || |  |||   ||||   |    ||| || ||   |      | ||| |  ||||| ||||| |||||  | ||  |||||||||| ||||||||||| || ||||||||||| || ||||| || || |||||| ||||  |
----------------------gtaaaacgatgcttcttttttcttttctccctctttcgttctgatttgagattcgtgaccagGCGACACT-TGCTTTCGTGGGTATGGGCGACGCGATGGTGAGCGGAGGAGGAAGTCAGTTCGTGGTTGCATTGTCAGCCATGATCTGTCTGTTCTCAATCT

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|31664073|gb|CD573253.1|CD573253
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|148942260|gb|EC887276.2|EC887276
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|32845854|gb|CD985535.1|CD985535
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|149075315|gb|EE163821.2|EE163821
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|16137351|gb|BI894216.1|BI894216
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGAG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|22521636|gb|BU080447.1|BU080447
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GCACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
EST: gi|29577181|gb|CB617293.1|CB617293
EST:     GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGG                         GGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA
genomic: GAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGA

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: 331

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 297

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT


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

GGTTATGTCTTCAAGATCATGGGTGGATGTGACAAGCAAGGCTTCCCAATGAAGCAAGGAGTTTTGACTTCTGGTCGTGTTCGTCTTCTGCTCCATAGGGgtatagagac ... aattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagcaccatcttttactctgattcttatctgaacattcgatatcaattctgtagGGACTCCCTGCTTCCGTGGTTATGGCAGGCGTAATGGTGAGCGCAGGAGGAAGTCTGTCCGTGGTTGCATCGTGAGCCAAGACCTATCTGTTATCAACTT
                ctctgat  putative branch site (score: 168)
                                        atatcaatt  TA-rich tract