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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgattttttacttcattgatggcattcagtatttcttataattcaaatatggcttacataatgtctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA

Basic information

species Zea mays
transcript GRMZM2G171604_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 5
gtgtgattttttacttcattgat-ggcattcagtatttcttataattcaaatatggcttaca----taatgtctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA
||||| |  ||| ||   || || || | |    || | ||| ||   || |||   ||  |    |||| |    ||||||||||||||||| ||||| |||||||| ||||||||||| ||||| || |||||||| |||||||||||||||||||||||||| |||
gtgtg-tcgtttgctcacttaataggtagtagccatcttttacaaactaattattctttgtactgataatttggctaaacagATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAA
















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|31356451|gb|CD440808.1|CD440808
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTCCAAGCGCTATTATTGACAAATACATTGGA
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGA
EST: gi|149076338|gb|EE164954.2|EE164954
EST:     CCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCCACTTTTTTGA-G                         ATTGTTTCAAGCGCTATTAT
genomic: CCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTT-GAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTAT
EST: gi|148999624|gb|EE036609.2|EE036609
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|149111231|gb|EE294729.2|EE294729
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|87157334|gb|DY402123.1|DY402123
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTNCA-GCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTT
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTT-CAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTT
EST: gi|211475166|gb|FL103099.1|FL103099
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|148936301|gb|EC880384.2|EC880384
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTNCA-GCGCTATTATTTGACAA-TACATTGGAGAAAGTGCTCGTT
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTT-CAAGCGCTATTATT-GACAAATACATTGGAGAAAGTGCTCGTT
EST: gi|93284400|gb|EB676664.1|EB676664
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|149080389|gb|EE169410.2|EE169410
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|148959843|gb|EE153075.2|EE153075
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTNCA-GCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTT
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTT-CAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTT
EST: gi|148953590|gb|EC898944.2|EC898944
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTNCA-GCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTT
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTT-CAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTT
EST: gi|22935727|gb|BU572002.1|BU572002
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCT
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCT
EST: gi|148967099|gb|EE018270.2|EE018270
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|148942358|gb|EC887376.2|EC887376
EST:     CCCTATTGGCAGGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGGGCTCG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCG
EST: gi|5325115|gb|AI783306.1|AI783306
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|211472646|gb|FL103083.1|FL103083
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|148931017|gb|EC873580.2|EC873580
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|67033051|gb|CO461800.1|CO461800
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|148979144|gb|EE026532.2|EE026532
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|67024916|gb|CO453665.1|CO453665
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|148964792|gb|EC906040.2|EC906040
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|149112655|gb|EE191390.2|EE191390
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|149100597|gb|EE186683.2|EE186683
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
EST: gi|149009942|gb|EE041784.2|EE041784
EST:     CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG                         ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG
genomic: CCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTG

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: 313

GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 254

GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 165

GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAGgtgtgatttt ... ctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcattcagtatttcttataattcaaatatggcttacataatgtctgaaaacagATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAA
                               ggcttac  putative branch site (score: 182)
        agtatttcttataatt  TA-rich tract