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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagctatcttgtttccccaattgttgaaataatacatttagaaattgggaagatgaaagaatagtgtttgcatttttgcatgcattgttgtcat...

Basic information

species Zea mays
transcript GRMZM2G115939_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 5'ss of exon 5
TGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagctatcttgtttccccaattgttgaaataatacatttagaaattgggaagatgaaagaatagtgtttgcatttttgcatgcattgttgtcat--
|||||||||||| ||||| || ||||||||| ||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||||||| |  ||||   ||| | |  ||| ||| ||  |||| | || | |  | |  ||| ||   | |   ||| ||| ||     ||||   |   
TGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCCTTAACCTTCTTTTTACGgtatttcagtttccttgac-ccctattgattgcaattatgtatttcggaaatagataaaaaaaacaaatatctaatcatgtttaca-atgctgttcaaacct

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT2G18600.1 (Arabidopsis thaliana), 5'ss of exon 5
TGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagctatcttgtttccccaat----tgttgaaataatacatttagaaattgggaagatgaaagaatagtgtttgcatttttgcatgcattgttgtcat
 ||| | ||||| || ||||||||||||||  |||||||||| ||||| || ||||||||||| ||||| ||||| || || ||    | ||| || ||||||    || | ||      |    ||      ||||  | ||  || | |    |   ||  |||| || | || ||    | ||||    ||| |       
CGATCTAGAAGGAAACGTCTGTCTGAACATCTTGCGTGAAGACTGGAAACCGGTTCTCAACATAAACACAGTTATCTACGGTCTTTTCCATCTCTTCACGgtaaca-agttctccctgaccgatgatactccattgatgttat-tatcttgggccttctaatctgaa-gacttgttttgctttgtttgttcacatag-------

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT4G36800.1 (Arabidopsis thaliana), 5'ss of exon 5
TGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagctatcttgtttccccaattgttgaaataatacatttagaaattgggaagatgaaagaatagtgtttgcatttttgcatgcattgttgtcat
 ||||||||||| || || || ||||||||  |||||||||||||||| |||||||| ||||| ||||| ||||| || || ||    | ||| || |||||| || | |      |||    |||     |   |  |   ||      ||    |  |||  || |  | ||  ||                      
CGATTTGGAAGGAAACGTTTGCCTGAACATCTTGCGTGAAGATTGGAAACCTGTTCTTAACATTAACACAGTTATCTACGGACTCTTCCATCTGTTCACGgtaatt-aaccggacagttcgatcaaacaaaggtttt-tgtgttatttggtttctgaactgagtgattgtttttcacacag-------------------

upper sequence: GRMZM2G115939_T04 (Zea mays), 5'ss of exon 5
lower sequence: PP1S61_126V6.1 (Physcomitrella patens), 5'ss of exon 5
TGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgta--tttcagctatcttgtttccccaattgttgaaataatacatttagaaattgggaagatgaaagaatagtgtttgcatttttgcatgcattgttgtcat
 ||| ||||||||||||| |||||||| ||||| ||||| |||||||||||||| || |   | ||| |  | || ||||| ||  |   ||| ||   ||||  |||| | |||  | | |       ||      |  |      | || |   |  |   | | ||  | ||  |  ||  || | |   | | | |  
AGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTCTCCAATATCTATTCTTGgtaggtttctgatattatctgttaatgtgtgaccttgtggtttgaaaataattcttggggtccagacaactgcgtg-gtgttaatg-aagtggtatagcctc

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|33093997|gb|CF053991.1|CF053991
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|32846744|gb|CD986425.1|CD986425
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|26455341|gb|CA826924.1|CA826924
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|32801453|gb|CD953689.1|CD953689
EST:     CTGTTCTCAACATCAACACTGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATC
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATC
EST: gi|8516672|gb|BE123397.1|BE123397
EST:     CTGTTCTCAGCATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211060519|gb|FL179753.1|FL179753
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|21330709|gb|BQ486090.1|BQ486090
EST:     CTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|32847082|gb|CD986763.1|CD986763
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211291785|gb|FL131028.1|FL131028
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|78077789|gb|DV506218.1|DV506218
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCCG
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCC-G
EST: gi|211320075|gb|FL327296.1|FL327296
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTYTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCC
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCC
EST: gi|211153912|gb|FL325451.1|FL325451
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAAC-AAACGACGAGGATCCTTTGAAACACGAAGCTGCATGCTGTCCTCCG
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCA-GCTGTCCTCCG
EST: gi|8516401|gb|BE123127.1|BE123127
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|50326390|gb|CO521516.1|CO521516
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCA
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCA
EST: gi|211407585|gb|FL360124.1|FL360124
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211291786|gb|FL131029.1|FL131029
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGA
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGA
EST: gi|78077788|gb|DV506217.1|DV506217
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211378878|gb|FL474247.1|FL474247
EST:     CCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|91875000|gb|EB404957.1|EB404957
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211441546|gb|FL398417.1|FL398417
EST:     TCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: TCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211291784|gb|FL131027.1|FL131027
EST:     CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|8516280|gb|BE123007.1|BE123007
EST:     CTGTTCTCAACATCAGCACCGTTATTTATGGCCTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
genomic: CTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGCTGTCCTCCGT
EST: gi|211090799|gb|FL312054.1|FL312054
EST:     GTTCTCAACATCAACACCCGTTATTTATGGCCNTGAATCTTCTTTTTACG                         CAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAGGCTGTCCTCCG
genomic: GTTCTCAACATCAACACC-GTTATTTATGGCC-TGAATCTTCTTTTTACGgtatttcagc ... ttacctgcagCAACCAAACGACGAGGATCCTTTGAACCACGAAGCTGCAG-CTGTCCTCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACGgtatttcagctatcttgtttccccaattgttgaaataatacatttagaaattgggaagatgaaagaatagtgtttgcatttttgcatgcattgttgtcat

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