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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcaaaaatcatattagcacaaccattaattctgcgtgtttctggtgaacctaatgtttcgcttgtgtgtgtgtttctttttttttttgcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG

Basic information

species Zea mays
transcript GRMZM2G102625_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102625_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g05230.1 (Oryza sativa), 3'ss of exon 6
--tatgcaaaaatcatattagcacaaccattaattctgcgtgtttctggtgaacctaatgtttcgcttgtgtgtgtgtttctttttttttttgcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG
| | | ||||| || |||| | | || | || ||| | | | | | || | ||| |||| ||||| ||||||| ||||||||||| ||||| |||||||| || || ||||||||||| |||| || || ||||||||||||||| |||| ||||| ||||||||||
ccttttcctgcatcattacagtacaattgt-agcgctctgcacttttgg-actcatgcaactaaaaacaaacattttttattccctttctttgaatttatagGTAACGGAACAACCATCAGCTCTTGAAGGTGGGGAGTTAAGACCATATCAATTAGAGGGCCTGCAATGGATGCTTTCTTTATTCAACAATAATTTGAATG

upper sequence: GRMZM2G102625_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G28120.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------------tatgcaaaaatcatattagcacaaccattaattctgcgt-gtttctggtgaacctaatgtttcgcttg-tgtgtgtgtttctttttttttttgcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG
| | || | | | || | | | || | ||| | |||| || | | || || | | | || || |||||||||||| || ||||| ||| || ||||||| ||||| |||||||| ||| |||| || |||||||||||||||||| | ||||| ||||| || ||||
gtaggaggattcctcatcctccaaatgcattgttgtattattttctgtttttatgaggttcttattttatcaaggaaaagaaaataaaaaagtcactccttattagttgtttctgaataaaagttgtagcacactggaaatataaccaacttagtt---gtttacagGTAACTGAGCAACCGTCTATGCTTCAAGGTGGAGAATTAAGACCATACCAGATAGAGGGGCTCCAATGGATGCTTTCTTTGTTTAATAACAACTTAAATG

upper sequence: GRMZM2G102625_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G39630.1 (Glycine max), 3'ss of exon 4
-tatgcaaaaatcatattagcacaaccattaattctgcgt-gtttctggtgaacctaatgtttcgcttg-tgtgtgtgtttctttttttttttgcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG
| | || | | | | || | ||| || | ||| | |||| || | | || || | | | || || |||||||||||| || ||||| ||| || ||||||| ||||| |||||||| ||| |||| || |||||||||||||||||| | ||||| ||||| || ||||
ttttatcaagaaaaagaaaataaaaaagtcaatccttattagttgtttctgaataaaagttgtagcacactggaaatataaccaacttaatt---gtttacagGTAACTGAGCAACCGTCTATGCTTCAAGGTGGAGAATTAAGACCATACCAGATAGAGGGGCTCCAATGGATGCTTTCTTTGTTTAATAACAACTTAAATG

upper sequence: GRMZM2G102625_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G00640.1 (Glycine max), 3'ss of exon 7
tatgcaaaaatcatattagcacaaccattaattctgcgtgtttctggtgaacctaatgtttcgcttgtgtgtgtgtttctttttttttttgc-atttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG
|| | | ||| || | | | | | | || |||| | | |||||||||||| || ||||||||| ||| ||||||| ||||| |||||||| || |||||||| ||||| |||||||||||| | ||||| |||||||| ||||
---------------------------gtaggtttctgtgatttacaaaattcaagagaattgtagtacaatggaattctaactagcataattatttacagGTAAGCGAGCAACCATCTATTCTTCAAGGTGGAGAATTAAGACCATACCAACTAGAAGGCCTCCAGTGGATGCTTTCTTTGTTTAATAACAATTTAAATG

upper sequence: GRMZM2G102625_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g02960.t01 (Vitis vinifera), 3'ss of exon 6
tatgcaaaaatcatattagcacaaccattaattctgcgtgtttctggtga-acctaatgtttcgcttgtgtgtgtgtttctttttttttttgcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG
| ||| | ||| || | | | | | |||| | | | || | | | | || ||| | | ||||||| || |||||| || || ||||||| ||||| |||||||| ||| ||||||| || ||||||||||| ||| | || || |||||| ||||||
-tttcaatgctgtgcttattgcattggtctttcattgctaatactggaaataacagatctactattaacaaaagaataatattaaatttcaaactctttagGTAACTGAGCAACCAGCTATGCTTCAAGGTGGAGAATTAAGACCATACCAGTTAGAAGGGCTTCAATGGATGCTCTCTTTGTTCAATAACAATCTGAATG

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: 225

TCCTTCAGATGACGATGGAGACCTCCCTGGCCCTGCAGATGAAAGTAAATTCAATGCAGGACGTAGACTTGATTTTACTGTTCATTCTATTGAAGAAAAGgtagcaaagt ... gcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 106

TCCTTCAGATGACGATGGAGACCTCCCTGGCCCTGCAGATGAAAGTAAATTCAATGCAGGACGTAGACTTGATTTTACTGTTCATTCTATTGAAGAAAAGgtagcaaagt ... gcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TCCTTCAGATGACGATGGAGACCTCCCTGGCCCTGCAGATGAAAGTAAATTCAATGCAGGACGTAGACTTGATTTTACTGTTCATTCTATTGAAGAAAAGgtagcaaagt ... gcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 209

TCCTTCAGATGACGATGGAGACCTCCCTGGCCCTGCAGATGAAAGTAAATTCAATGCAGGACGTAGACTTGATTTTACTGTTCATTCTATTGAAGAAAAGgtagcaaagt ... gcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgaacctaatgtttcgcttgtgtgtgtgtttctttttttttttgcatttacagGTAACAGAACAACCATCTGCTCTCGAAGGTGGTGAATTGAGACCATATCAGCTAGAAGGTCTCCAATGGATGCTTTCTCTATTTAACAACAATTTGAATG
     acctaat  putative branch site (score: 209)
 tgtttctttttttttt  putative PPT
 tttctttttttttttg  TA-rich tract