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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaactcatgggctcatggcattgcatagtgtattaggttgtctttgaaaatctcatgtgaacatgcttacctgaagattttgttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG

Basic information

species Zea mays
transcript GRMZM2G117786_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 3'ss of exon 3
gtatggaactcatgggctcatggcattgcatagtgtattaggttgtctttgaaaatctcatgtgaac-atgcttacctgaagattttgttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG
|||| | || || || || | ||| | || ||||||| | || || | |||||||||||| || || | ||||||||| ||||||||||| |||||||||||||||||||| ||| | ||||||||||| |||||||||||||||
---------gtatggaacc-tgatgtttca--gtcttgtagatcgttgttgaaaaacatgtgaaaattgtacttacctgaagaattggtggtctgcagGGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG

upper sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 3
--gtatggaactcatgggctcatggcattgcat-agtgtattaggttgtctttgaaaatctcatgtgaacatgcttacctgaa---gattttgttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG
|| | | || | | | | | || || | | | || ||||| | ||| || | ||| || ||| || | |||| ||||| || || ||||| |||||||||||||| || || |||||||||| || |||||||| ||||||
gtgtctttatgaattgtgattgttgtttgttattagcaaaaaaaaatttcgttgaac-ttgggtgttttaattttgacccaaatttaattgtgcctgctacagGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAG

upper sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------gtatggaactcatgggctcatggcattgcatagtgtattaggttgtctttgaaaatctcatgtgaacatgcttacctgaagattttgttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG
| | || | | ||| | || | | | | ||||| | | | |||| ||| | || | | | ||||||| || || |||||||| ||||| |||||||||||||| |||||||||| || || || ||||| |||
gttttcattgtttaatttttctgtgtcttctcctctctatacggttttggggc-acttaaaatgtgggttgttctttcttcttttggagcaaacaaaattaagttgtacttctcattcatccagGGACCTTCACTCTGTCCAATTTGGGCATGTTTGGTGTAGACAGGTTTGATGCTATTCTGCCTCCTGGTCAG

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|5895843|gb|AW037089.1|AW037089
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|91049207|gb|EB159625.1|EB159625
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|5936720|gb|AW059988.1|AW059988
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACCCTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|5770188|gb|AI973362.1|AI973362
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|91869380|gb|EB400357.1|EB400357
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|6526785|gb|AW216060.1|AW216060
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|32932202|gb|CF037014.1|CF037014
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|110529248|gb|EE033432.1|EE033432
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTTTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|4885756|gb|AI676876.1|AI676876
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|149108974|gb|EE189934.2|EE189934
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|32932221|gb|CF037033.1|CF037033
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|71767883|gb|DR965820.1|DR965820
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|38687553|gb|CK144584.1|CK144584
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|31354698|gb|CD439055.1|CD439055
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|6466738|gb|AW191398.1|AW191398
EST:     AGTCAAGAAAGCNCGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTNCACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|5325071|gb|AI783262.1|AI783262
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|91053207|gb|EB163625.1|EB163625
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|60396288|gb|DN229157.1|DN229157
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|76013819|gb|DT940989.1|DT940989
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|91056736|gb|EB167154.1|EB167154
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|71763414|gb|DR961351.1|DR961351
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|74236495|gb|DT644409.1|DT644409
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|30088033|gb|CB886238.1|CB886238
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|148960322|gb|EE153578.2|EE153578
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|24768545|gb|CA403674.1|CA403674
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|149085129|gb|EE174634.2|EE174634
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|78021875|gb|DV490262.1|DV490262
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|76016286|gb|DT943456.1|DT943456
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|5846883|gb|AI999966.1|AI999966
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
EST: gi|78083530|gb|DV511923.1|DV511923
EST:     AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG                         GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG
genomic: AGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATG

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: 80

CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTGgtatggaact ... ttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctttgaaaatctcatgtgaacatgcttacctgaagattttgttatttgcagGGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAG
                          tgcttac  putative branch site (score: 206)
 ttttgtt  putative PPT
 aagattttgttattt  TA-rich tract