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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactgaaaatgcaaaattgtttgaagttaattcttaatcgtcaacactatttgattctaatgtactttttttctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG

Basic information

species Zea mays
transcript GRMZM2G016184_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 6
gtaag-aaactgaaaatgcaaaattgtttgaagttaattcttaatcgtcaacactatttgattctaatg------tactttttttctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG
||||| ||  |||  |||    |||  ||| |   | |  ||  || ||     |||||| || |||        | ||    ||  ||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||||||||||||
gtaagcaagttgagcatgtttcatttcttgtatgaagtcatt--tcatctcagttatttggttataacattctgatgctcggatttattttaagGTTTCTTGACACAGCTGGACTGAAAAAGTCAAGTGCTTACTTGGTTAATGGTATTCTGATGTTCGTTGCATGGCTG
















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|37375483|gb|CF624180.1|CF624180
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|211033261|gb|FL440337.1|FL440337
EST:     TCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|6465580|gb|AW191175.1|AW191175
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|86474267|gb|DY240637.1|DY240637
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|6526808|gb|AW216077.1|AW216077
EST:     CCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGGTAATGG
genomic: CCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|32910942|gb|CF015754.1|CF015754
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|60400317|gb|DN233124.1|DN233124
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|148953652|gb|EC899011.2|EC899011
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|83279176|gb|DV943184.1|DV943184
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|211286255|gb|FL063748.1|FL063748
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|67030326|gb|CO459075.1|CO459075
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|76293602|gb|DV033170.1|DV033170
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
EST: gi|83278187|gb|DV942195.1|DV942195
EST:     TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATG                         GTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG
genomic: TACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGG

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: 244

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 109

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

TGGTTGCAATAGCTTACACAATGTTGTCTGGGGAAGGGCAGTTTTACACATACATGGTTCTCATTTCAGAGACAACCACCCCTGAAATCAACTTGCGATGgtaagaaact ... tctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattcttaatcgtcaacactatttgattctaatgtactttttttctttttaagGTTTCTTGACACTGCTGGACTGAAGAAATCAAGTGCTTACTTGGTTAATGGAATTCTGATGTTTGTTGCATGGCTG
                            ttctaat  putative branch site (score: 214)
                                  tgtactttttttcttt  CT-rich tract
                           attctaatgtactttt  TA-rich tract