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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 34
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 34
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 51
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGT---CATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG
                | ||   | |  |   |      ||||  |      || | | || | | |||| ||| |  || | ||| ||||| |  | |||||| || |||||||| ||||||||| |||||||||||||||||||||| ||| | |||    ||||||| |||| ||||||||| || ||| | || ||      
----------------gtctgccttctgtcatacttgctgttaagctgcacttctaagctt-tataatctgattgtatgaattgttctttctat-gccagCAGGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCAT------

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 34
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTC---ATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG
                | ||   | |  |   |      ||||  |      || | | || | | |||| ||| |  || | ||| ||||| |  | |||||| || |||||||| ||||||||| |||||||||||||||||||||| ||| | |||    ||||||| |||| ||||||||| || ||| | || |||||   
----------------gtctgccttctgtcatacttgctgttaagctgcacttctaagctt-tataatctgattgtatgaattgttctttctat-gccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA---
















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|71440205|gb|DR821255.1|DR821255
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
EST: gi|211104807|gb|FL044860.1|FL044860
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
EST: gi|60398867|gb|DN231683.1|DN231683
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     AGGTCAAGGTGACGCCACTGACCAACANACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTTAGGAAAAGGATGAAA-GCATTCAAGCTGCAGCT
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTT-AGGGAAAGGATGAAAAGCATTCAAGCTGCAGCT
EST: gi|76285312|gb|DV024880.1|DV024880
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     AGGTCAAGGTGACGCCACTGACCAACANACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTANGGAAAGGATGAANAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
EST: gi|211409478|gb|FL448716.1|FL448716
EST:     AAACTGATAGATACCAG-CCTTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCT
genomic: AAACTGATAGATACCAGACC-TCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCT
EST: gi|60347986|gb|DN214959.1|DN214959
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
EST: gi|83278453|gb|DV942461.1|DV942461
EST:     AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAG                         GTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA
genomic: AGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTA

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: 176

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCTTTCAGAGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCTTTCAGAGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCTTTCAGAGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCTTTCAGAGGTCAAGGTGACGCCACTGACCAACAAACTGATAGATACCAGACCTCAGgtccccattc ... ttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG
                                ttcgttatttctttt  CT-rich tract
                     ttattattagattcgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccccattctacacagcctcagtgcatttgcatgcatagttatacatgctatcaatgtttatgtgatcttattattagattcgttatttcttttacgagcagGTACATTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCTGCAGCTATAGGTCATTTTGACGGAGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA