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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaaactattttttggatatgctgtcatttcattcttttacgcacaaaatgcacaataccaatttaacaccatttatgtgtccattgcttgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC

Basic information

species Zea mays
transcript GRMZM2G147811_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 8
gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaaactattttttggatatgctgtcatttcattcttttacgcacaaaatgcacaataccaat--ttaacaccatttatgtgtccattgcttg-tattct--agGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC
| || | | ||| |||| | | |||| | ||| || | | || || | | | |||| | ||| | | | |||| |||||| ||||||||||||||||||||||||| ||| | |||||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| |||||||||||||
----------------------------------------------------------------------------------ttgaaca----tgcttgaatat--ttttatttatgcttgttatatactacagtcattgtatctacagtaaacatcctttttaattttttgtcttgatattctttagGTGAATGAGGCTAAGAATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATC

upper sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 13
gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaaactattttttggatatgctgtcatttcattcttttacgcacaaaatgcacaataccaatttaacaccatttatgtgtcca-ttgcttgtatt--ctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC
| | || || | | | ||| | | | | | || | ||| ||| | | |||| | ||| | |||||| | | || || | | | || |||| |||||| |||| ||||| | ||| | ||||| |||||||| || ||| ||||||||| ||||||||||| || |||||||| || ||||| ||||
------------------------------------------------------------------------gtatgcctaaattactgttgtgtttagattgtttcttttcctagttttgttaatttcaagaaga--aatatctattatctaacatttagttcttcaatttcctcttttgataagGTAAATGAGTCTAAAAATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC

upper sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G24820.2 (Glycine max), 3'ss of exon 10
gtacgccatctttgcttgtcatcatttttaattatagtattattgcaagttctctttctcaacaggaattgcatcttaatacataaaa-actattttttggatatgctgtcatttcattcttttacgcacaaaatgcac-----aataccaatttaacaccatttatgtgtcca-ttgcttgtatt--ctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC
|| | ||||| ||| || | | | || | || ||||| |||| || | || |||| | |||| | |||||| | | || || | | | || | |||| ||||||||||||||||| | ||| | ||||| ||||| || || ||| ||||||||| ||||||||||| || |||||||| || ||||| ||||
----------------------------------------------------------------------------gtatgcctaaaatactgttgtgtttagattgtttcttttcaaaattttgtttgttaatttcaagaagaaatatctattttctaacatttagttcttcaatttcctcttttgacaagGTAAATGAGGCTAAGAATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATC

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|67021773|gb|CO450522.1|CO450522
EST:     TGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTG                         GTGAATGAGGCTAANAATGTGCTCAAGGTATGTGATTNTGGGCA-CGCTAT
genomic: TGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTGgtacgccatc ... tgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGG-CAACGCTAT
EST: gi|32945651|gb|CF050470.1|CF050470
EST:     TGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTG                         GTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATG
genomic: TGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTGgtacgccatc ... tgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATG

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: 42 (upstream exon), 48 (downstream exon)
Score: 66

GACTGCGGTGAGGGCATATTCAAAGCAGCTTTTCATCGCCCTGAAGCACCTGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTGgtacgccatc ... tgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 58

GACTGCGGTGAGGGCATATTCAAAGCAGCTTTTCATCGCCCTGAAGCACCTGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTGgtacgccatc ... tgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 66

GACTGCGGTGAGGGCATATTCAAAGCAGCTTTTCATCGCCCTGAAGCACCTGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTGgtacgccatc ... tgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 68

GACTGCGGTGAGGGCATATTCAAAGCAGCTTTTCATCGCCCTGAAGCACCTGAAGAACTGCAAAGTTTTGCACTGTGATATAAAACCAGATAATATGCTGgtacgccatc ... tgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaatgcacaataccaatttaacaccatttatgtgtccattgcttgtattctagGTGAATGAGGCTAAGAATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATC
                 atttaac  putative branch site (score: 68)
 aatttaaca  TA-rich tract