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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagacattctatttatgttcactttaaccctactatatatgtgtagccagtttgtaatgcattcatccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA

Basic information

species Zea mays
transcript GRMZM2G106140_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 8
gtaagtagacattctatttatgttcactttaaccctactatatatgtgtagccagtttgtaatgcattcatc-cttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA
||||| |  ||  ||||||||||| | |  |||  |  | ||| |||  || || | | ||||||||   ||  || |||||||||| |||||||| ||||| ||||| ||||||  ||||||||| || |||||||| ||||||||||| |||||||||||||||||| | ||||| ||  
gtaagaattcaagctatttatgtttaat--aactttgatgtat-tgtcaagtcaatatctaatgcatctgtcatttttacagTATGGCCATTTCTTCCCTGATCCTCAATATGAACATGTGCAACATATCATCTGCTGCGATTCATTTGCTACTTATGCATATGACTTTAACTTTTCACACC

upper sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G27460.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------gtaagtagacattctatttatgttcactttaaccctactatatatgtgtagccagtttgtaatgcattcatccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA
                  ||    |  |||   | ||| |   |||     |  | | | ||  |   ||| |   | |  |  | | |||   |||| ||| || |||||||| || || ||||| || |   | || || || |||||||||||||||| ||| || ||||||||||||||||| ||| |  |||
gtatgtggttttagtgaaaaccgaaagttcagataatgattttttttttttttttttttttgctt---cagctaacagtttagccttactt--gcagTTTGGTCACTTCTTTCCAGATCCACAGTACGAGAACCTTCAGCATATCATCTGCTGTGATTCATATGCAACATATGCATATGACTTTGAATTTGCAGATA

upper sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0080g00510.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtagacattctat-----ttatgttcactttaaccctactata---tatgtgtagccagtttgtaatgcattcatccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA
|| |||   |||   ||     ||| | |     || |  |  || |   | | | |      |||  | |    | |   || | |||||||| |||||||| || || || ||||| |||| ||||||||||||||| || |||||||| | || ||| ||||| || || ||||| ||| || | |
gtgagtgatcatatcatgtcctttaagattgtcatagctgtgttacactttgtttattttacatttacacttacattaaatttttgcagTATGGTCATTTCTTCCCAGATCCACAGTACGAAAATGTGCAACACATTATTTGTTGTGATTCTTATGTCACATATGCCTACGATTTTGATTTTGCCAACA

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|71314648|gb|DR793946.1|DR793946
EST:     GTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT                         TATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATC
genomic: GTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCTgtaagtagac ... ccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATC




















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: 47 (upstream exon), 49 (downstream exon)
Score: 121

ATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCTgtaagtagac ... ccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

ATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCTgtaagtagac ... ccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 93

ATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCTgtaagtagac ... ccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 131

ATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCTgtaagtagac ... ccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaaccctactatatatgtgtagccagtttgtaatgcattcatccttctacagTATGGACATTTCTTTCCTGACCCTCAGTATGAAAGTGTGCAACACATTATCTGCTGTGATTCATTTGCCACTTATGCATATGACTTTGAGTTTTCCCATA
 ctttaac  putative branch site (score: 131)
                                        ttcatccttct  putative PPT
         tactatatat  TA-rich tract