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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttatgtctgcaaagaatgtaaattgtctattgttactaagcacatatattttgtattgctaactccttgcccacatcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG

Basic information

species Zea mays
transcript GRMZM2G090738_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 4
gtatatttat-gtctgca-aagaatgtaaattgtctatt---gttactaagcacatatattttgtattgctaactccttgcccacatcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG
|||  ||  |   ||| |  |  ||| | | ||    ||    || ||     |||| | |||  ||| ||  ||  ||     |||  | |||| |||||||||||  | ||| ||||||||||||| |||| | |||||| |||||| |||||||| |||||||||||||||
gtagtttcctcagctgaatgaatatgcagaatgctggtttgtcttgctgtatgcatacaattta-attcct--ctgttttgatgcattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG

upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 4
gtatatttatgtctgcaaagaat--gtaaattgtctatt---gttactaagcacatatattttgtattgctaactccttgcccacatcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG
|||  ||  |   |  || ||||  | | | ||    ||   ||| ||      ||  | |||  ||| ||  ||  ||     |||  | |||| || ||||||||  | ||||||||||| ||||| |||||| |||||| |||||| |||||||| ||||||||| |||||
gtagtttcctcagttgaatgaatacgcagaatgctggtttgtgttgctgtatgaatgcaattta-attcct--ctgttttgatgcattgtgtagCTTATTGCACTGGCTTGCTTTTGGCTCGCCGTGTGCTCAAGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATATTGAG

upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatatttatgtctgcaaagaatgtaaattgtctattgttactaagcacatatattttgtattgctaactccttgcccacatctt-ctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG
   |||| |         | | | |   ||  | | | ||          | |||  | | ||    |||   ||      || | ||||| ||||| ||||| ||||||||||||||||||||||| || || |  ||  ||||| | ||||| ||||| || || |||
--gtattgaatcagttctatacttttgttttcccaatatttgattctgtgtgtatggtttcttaaagacttaatgtttttgtcatgctagCTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAG

upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 3
--gtatatttatgtctgcaaagaatgtaaatt----gtctattgttactaagcaca---tatattttgtattgctaactccttgcccacatcttcta----------gCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG
     |||| |  | |  |  || | |  | |      || |||||  | |  ||    |   |||    ||| |   |   || | |    || ||          || ||||||||||||||||||||||||||||||  | | ||||     || ||||| |||||||| |  |||||||    |
gtacgtattcacttgtctagtgattttttactcccgaccttttgtttttgacaacggtcttcctttccgtttgtttgtttgatgtcaatggtttgtattggtgcgcagCTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACG

upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S38_329V6.2 (Physcomitrella patens), 3'ss of exon 4
gtatattt---atgtctgcaaagaatgt-aaattgtctattgttactaag-----caca-tatattttgtattgctaactc-----------cttgcccacatcttct--------agCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG
||| |||    |  | |  |   ||| | |||| ||||  | || ||        |||| ||  |||| || || | ||             |||| |  || ||  |        ||| || ||||||||||||||||||||||||||   | | |||| |   || ||||||||||||||||  || || |    |
gtacattctcaacctatcaacgcaatatgaaatcgtctccttttccttctgtcttcacaataccttttatagtggtcacctggctaggagatcttgacgtcaactgttctgtatgcagCATATTGCACTGGTCTTCTTTTGGCTCGTCGGCATTTGAAGAACTTCGAGTTGGATCAGGAGTATGTTGGGAACGAGACG

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|211279083|gb|FL069189.1|FL069189
EST:     TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAG                         CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
genomic: TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
EST: gi|32846847|gb|CD986528.1|CD986528
EST:     TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAG                         CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
genomic: TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
EST: gi|211279085|gb|FL069191.1|FL069191
EST:     TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAG                         CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
genomic: TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
EST: gi|211279081|gb|FL069187.1|FL069187
EST:     TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAG                         CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
genomic: TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
EST: gi|67024091|gb|CO452840.1|CO452840
EST:     TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAG                         CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
genomic: TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
EST: gi|60672209|gb|DN474977.1|DN474977
EST:     TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAG                         CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT
genomic: TGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATT

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: 508

GTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 375

GTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 656

GTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 365

GTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttat ... catcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttactaagcacatatattttgtattgctaactccttgcccacatcttctagCCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG
                            tgctaac  putative branch site (score: 365)
                                             catcttct  putative PPT
             acatatattttgtatt  TA-rich tract