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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaataaaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttatctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG

Basic information

species Zea mays
transcript GRMZM2G373175_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 2
---tgcaataaaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaa-gttatatcttgacgtcctttcataaaaaacggttttatctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
    | |     |||  |  ||  |       | | ||  ||| ||   |  |    || |||   || | || | |||      |   |  ||||||  | ||||||| || |||||||| |||||||  ||||| ||||||||||| ||||||||||||||| | |||||||| ||||||||||||||||||||||||||||
atcagtagggttattcataagagagatcctaacctagcc-tagattaaagcatcttattttattaggatggccct-cattggttgca--tacatctcatttcagGGTTTCACTTATCCTGTTCGGAGTCGATTTCTAGAAGATATTCTCGAAATTACTGGGCACAGATTAACTCCTTACAATCAAATTGATGACTATGGTCAAG

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 3
tgcaataaaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttatctc-aacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
     |    ||| |||||   |  || || || || |   |   | || ||| || |  ||  |     ||  |       | | | ||  | ||  |||||||| ||||| |||||  | | ||| ||| |||| |||||||| |||||  | ||  || | || |||||  |||||||||||||||||||||||||||
ctattttgtttttatttgatgttactgagcattactatt-ttggctctgaaagctaaaagtttcccattcttattgtttggggatgtgatggctaatatagGGTTTCACATACCCTGTTAGAACTCAATTTTTGGAGGATATTCTGGAAATGTCGGGCTACAGATTGACTCCTGACAATCAAATTGATGACTATGGTCAAG

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G34180.1 (Glycine max), 3'ss of exon 8
---tgcaata--aaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttatctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
   |||  |   ||||   | || || |  |      |  | |      |    |||  | ||| ||    |  |||  |    | | ||    | ||    ||||||||||||| ||| || ||    |||||||| || || ||||| ||||  |||||  |  | || || || || |||||||||||||||||||||||||
tgttgctctggcaaatcgatatgcatttgcttacagataatatgaaagatatgataaact-tattttattttaattttctggggacctgtgcactttc----tagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGACATTCTGGAAAGGACTGGATATCGATTGACACCGTATAATCAAATTGATGACTATGGTCAAG

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 8
tgcaataaaatttgtttgaatgtcttgtgctttgctgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttat-ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
||             | ||    | | |||||    ||    |      || | || | |||    || ||| ||       ||   | | | |    ||||||||||||| ||| || ||    |||||||| || |||||||| ||||  |||||  |  |||| || || |  |||||||||||||||||||||||||
tgttgctttgacaaatcgatatacatttgcttacaggtgatatgaaagatatgata-aacttattttcttttaattttttggggacctgtgcactttctagGGTTTTACATTTCCAGTTCGAGCACATTTTCTTGAGGATATTCTGGAAAGGACTGGATATCGGTTGACACCTTCTAATCAAATTGATGACTATGGTCAAG

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------tgcaataaaatttgtttgaatgtcttgtgctttgctg----tagcttcttgtgtaagt-tatatcttgacgtcctttcataaaa-----aacggttttatctcaact-tagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
                            |  || ||  | |    || | |  |  |||||||     |   |    || |  | |||    |||    |     | |||     ||   | |  |||  ||| ||||| ||||||||||| || || |||||||| || || |||||||| || || ||  || || | || ||||||||||||||||||||||| ||||||||||
gtaagtaagaaacatatttgtttatcctctttagaacatttcaagatatttaatcttttgctgagttcaatattccttggatctatatgctctgattaaccccagtgaaactactaatattgtcttcttcactatagGGATTTACATATCCAGTTCGTAGTCATTTCCTAGAGGATATTCTGGAGATGACCCGGTACAGATTGACTCCATACAATCAAATTGATGATTATGGTCAAG

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 7
--tgcaataaaattt-gtttgaatgtcttgtgctttgc-tgtagcttcttgtgtaagttatatcttgacgtcctttcataaaaaacggttttatctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
  |    ||  |||  ||   ||| | || |   |  | ||| | |  ||      || ||    | ||     |   |      |  |  | |   |  |||||| ||||| || || || || | ||||||||||||| ||||||| ||||| |||||  |  | || ||||| || |||||||||||||| ||||||||||
tttagtttattattgagtacaaattttttatatataacatgttgttcattcatggtgtgatggactaactcttctctctcc----ctctactgttctactttagGGGTTTACGTACCCAGTACGAACTCATTTTCTGGAAAATATTCTGGAAATGACTGGATATAGATTGACTCCTTATAATCAAATTGATGATTATGGTCAAG

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|31351858|gb|CD436215.1|CD436215
EST:     CTGAGCTATTCTCTTCATACTTTGGTGGAGCACCCATGATACATATACCT                         GGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATT
genomic: CTGAGCTATTCTCTTCATACTTTGGTGGAGCACCCATGATACATATACCTgtaagatatt ... ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATT




















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), 49 (downstream exon)
Score: 45

TCCACGTCGCCCTGAGCTGAGGCTTATATTGATGAGTGCAACCCTTAATGCTGAGCTATTCTCTTCATACTTTGGTGGAGCACCCATGATACATATACCTgtaagatatt ... ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 39

TCCACGTCGCCCTGAGCTGAGGCTTATATTGATGAGTGCAACCCTTAATGCTGAGCTATTCTCTTCATACTTTGGTGGAGCACCCATGATACATATACCTgtaagatatt ... ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 22

TCCACGTCGCCCTGAGCTGAGGCTTATATTGATGAGTGCAACCCTTAATGCTGAGCTATTCTCTTCATACTTTGGTGGAGCACCCATGATACATATACCTgtaagatatt ... ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 63

TCCACGTCGCCCTGAGCTGAGGCTTATATTGATGAGTGCAACCCTTAATGCTGAGCTATTCTCTTCATACTTTGGTGGAGCACCCATGATACATATACCTgtaagatatt ... ctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtaagttatatcttgacgtcctttcataaaaaacggttttatctcaacttagGGTTTTACATATCCTGTCCGGAGTCATTTTCTGGAAGATATTCTTGAAATTACTGGGCACTGGTTAACTCCATACAATCAAATTGATGACTATGGTCAAG
             tcttgac  putative branch site (score: 63)
                                       ttttatctc  putative PPT
                        tttcataaaaaa  TA-rich tract