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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaaaatatcttgcatcttaaagatagtttgtttatgaacatgcattggcttcttttctgtcatgtccatgtgcaattgtccacttccatctctaattcctaatgcacttcatatgctctctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC

Basic information

species Zea mays
transcript GRMZM2G174107_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 5
gtaacta-aaatatct---tgcatcttaaagatagtttgtttat-gaacatgcattggcttcttttctgtcatgtccat-gtgc-aattgtc---cacttccatctctaattcctaatgcacttcatatgctctctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC
|||| |   ||||| |   ||  |   |||   |  || | ||| | | | |   ||||||  | | ||   | |  || |||   ||| ||   || | |  |  ||| |||||||| ||||||||     ||  |    ||||||||  | |||||| ||||||| ||||| ||||| || |||||||||||||||||||||||||||||| ||||| | ||||||||  ||||||| ||||
gtaattgtgaatatataaatgtgttacaaaataatgttatatattggatagg---tggctttatgtgtgaactatttattgtgttgattatcttgcattgctgta-ctacttcctaatccacttcattattcctactcaagcagGAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTTTTCCTTTTGGCCCCTGTTGCCTTCCTAACAGAAGGCATCAAAATCACTC
















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|32842413|gb|CD982094.1|CD982094
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|60351427|gb|DN218400.1|DN218400
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|60354172|gb|DN221145.1|DN221145
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|16378321|gb|BI992391.1|BI992391
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|16377738|gb|BI992093.1|BI992093
EST:     CCCTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|32840783|gb|CD980464.1|CD980464
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|13178610|gb|BG349868.1|BG349868
EST:     CCCTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|32941693|gb|CF046512.1|CF046512
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|13558927|gb|BG550282.1|BG550282
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACA
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACA
EST: gi|32940452|gb|CF045271.1|CF045271
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|148937400|gb|EC881580.2|EC881580
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|5688709|gb|AI941724.1|AI941724
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|15313742|gb|BI478935.1|BI478935
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|211517932|gb|FL479804.1|FL479804
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|148940598|gb|EC885404.2|EC885404
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|83279370|gb|DV943378.1|DV943378
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|56462047|gb|CK986345.1|CK986345
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|24934366|gb|CA452584.1|CA452584
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|13126160|gb|BG316730.1|BG316730
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
EST: gi|4624425|gb|AI615258.1|AI615258
EST:     CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAG                         GAATCCTTGGNCAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT
genomic: CCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTT

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: 52

GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 509

GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC


Block sizes: 41 (upstream exon), 27 (downstream exon)
Score: 9

GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GGCTGGCTTTTGGAGTGCAATGGCTTCAAATGTTACCTTTCAATCCCGAAATGTATTGAGCAAGAAGCTCATGGTTAAGAAAGAGgtaactaaaa ... ctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtccacttccatctctaattcctaatgcacttcatatgctctctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC
                      tcctaat  putative branch site (score: 178)
                                     tatgctctctttcc  putative PPT
                tctaatt  TA-rich tract