Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatggacaatttattttattctccatttctattttaatgcaattctgcataccctactgaaatatccgggttactgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG

Basic information

species Zea mays
transcript GRMZM2G036534_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 3'ss of exon 4
gtaagatggacaatttat--tttattctccatttctattttaatgcaatt--ctgcataccctactgaaatatccgggttactgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG
|||||| | |   |  ||  |||| | || |||   |||  |||||   |  ||||||    ||    | ||||    || |||||||||||| |||||||||||||| ||  ||||| |||| ||| |||||||||||||||| ||||| || |||||||||| ||||||||||
gtaagacgaaatttccatcttttaatttctattatcattc-aatgctgcttgctgcatgatttatgttattatctttattgctgaaaacagGGTGCAATCATGGCCGTTGGATCATCACAACCAACACTTGTTGGTACAAAAGATGGTAGTATTGGGATCAAGAACCAAATGCAG
















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|6539042|gb|AW225181.1|AW225181
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|6865176|gb|AW360526.1|AW360526
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|78106198|gb|DV524616.1|DV524616
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|23357491|gb|BU645140.1|BU645140
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|24768304|gb|CA403433.1|CA403433
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|6448387|gb|AW181153.1|AW181153
EST:     AATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: AATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|211440164|gb|FL434174.1|FL434174
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|6022391|gb|AW067319.1|AW067319
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|71765103|gb|DR963040.1|DR963040
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|60344293|gb|DN211266.1|DN211266
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|78088435|gb|DV516828.1|DV516828
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|149027250|gb|EE046447.2|EE046447
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|93013412|gb|EB638932.1|EB638932
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|71444183|gb|DR825233.1|DR825233
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGACCCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|93284411|gb|EB676675.1|EB676675
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|83279414|gb|DV943422.1|DV943422
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|74246257|gb|DT654171.1|DT654171
EST:     TTGGTATGTTTGGAGTTGATAGGTTGGATGCAATACTGCCCCCTGGAACT                         GGGGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|78074314|gb|DV502748.1|DV502748
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|71759734|gb|DR957671.1|DR957671
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTAC-AAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|74236968|gb|DT644882.1|DT644882
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
EST: gi|149035803|gb|EE155127.2|EE155127
EST:     TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT                         GGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA
genomic: TTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAA

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), 48 (downstream exon)
Score: 204

GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 175

GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 98

GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 539

GCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACTgtaagatgga ... ctgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattttaatgcaattctgcataccctactgaaatatccgggttactgaaaacagGGCGCAATCATGGCCGTCGGTGCATCAGAACCGACAGTTGTTGGTACAAAAGACGGTAGAATCGGGATCAAGAGCCAAATGCAG
   ttttaat  putative branch site (score: 539)
                             tgaaatat  TA-rich tract