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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgctgagttctgcattgcccactgctttcatatgattgtggttgaactcgatagtgtaactgcttgtggtaagattattgttcacatattcgttggtcgttgctgtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG

Basic information

species Zea mays
transcript GRMZM2G134256_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134256_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70170.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------gtaattgctgagttctgcattgcccactgctttcatatgattgtggttgaactcgatagtgtaactgcttgtggtaagattattgttcacatattcgttggtcgttgctgtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG
                                                  ||   |||| | | ||  |     ||||||        |     | ||| || |  |   ||||   |  || |||| || ||| | ||| |||| ||| |      |||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | ||||| || ||||| ||||| ||||||||| |||||||||| || || || |
gtaagtcctgattcctagtatttccattgttttttttccaccttagtcattatcagctgtgctgtgtttatttgactgctcaagacatacaaccgctgagcttgcca---taacccttgatgctaagcttgttgataacaaattcattgct------tgtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGATGGACTTGAGGCCTCTGGTTTGAGTGACCTATCCCGAGTGACCAGTGTAG

upper sequence: GRMZM2G134256_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 4
gtaattgctgagttctgcattgcccactgctttcatatgattgtggttgaactcgatagtgtaactgcttgtggtaagattattgttcacatattcgttggtcgttgctgtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG
               |   |   ||| | ||  | | || | ||  | |  || | | |||   ||| || |  ||  || |   |||  |   || ||    |||   |  |   |||||||| |||||  |  | |||||||| ||||| |||||||||||| | |||||||| |||||||||||  | |||||| | ||| | ||||| || ||||
---------------tttttcctccaat-ctcacttgtggtagta-tagtccttggt-gtgcttctgtttttcttataat-agcattctaaccatcattttctgttatggatgtgccagCTTATATTCTCTCTCCCGAGATATGAAGCTGTCATTGATGCTTACTTAGATGGGCTTGAGGCTTCTGGGCTAAGTGACCTCTCCAGGGTTACAAGTGTTG
















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|40335818|gb|CK369888.1|CK369888
EST:     GAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: GAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|60357531|gb|DN224504.1|DN224504
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|6626605|gb|AW258137.1|AW258137
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAATGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|5928815|gb|AW056107.1|AW056107
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|32831538|gb|CD971216.1|CD971216
EST:     TCCCTTC-ATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGA
genomic: TCC-TTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGA
EST: gi|32840664|gb|CD980345.1|CD980345
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|32841693|gb|CD981374.1|CD981374
EST:     TTCCTTCCATCCAGGAAGNTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATAT
EST: gi|32839772|gb|CD979453.1|CD979453
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|32865467|gb|CF005149.1|CF005149
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT
EST: gi|32848855|gb|CD988536.1|CD988536
EST:     TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACG                         CTTATTTTCTCAATTGCGAGATATGAGGCTGTGATTGATGCTTACCTCGAT
genomic: TTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGAT

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: 301

GGTCAACCGCCCCAATGTCTACATAAAGATCCCAGCTACTGCAGAATGTGTTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 779

GGTCAACCGCCCCAATGTCTACATAAAGATCCCAGCTACTGCAGAATGTGTTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 732

GGTCAACCGCCCCAATGTCTACATAAAGATCCCAGCTACTGCAGAATGTGTTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 609

GGTCAACCGCCCCAATGTCTACATAAAGATCCCAGCTACTGCAGAATGTGTTCCTTCCATCCAGGAAGTTATCGCTAATGGCATTAGCGTCAACGTCACGgtaattgctg ... gtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcttgtggtaagattattgttcacatattcgttggtcgttgctgtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG
          taagattatt  TA-rich tract