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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgcataggcatagacacgtccttgaattagtgtgatgatttactgttccgctgtgttggttcatttgcttggccttcacttgcggtgtgttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA

Basic information

species Zea mays
transcript GRMZM2G457881_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G457881_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g49730.3 (Oryza sativa), 3'ss of exon 1
cacgcataggcatag-acacgtccttgaattagtgtgatgatttactgttccgctgtgttggttcat-ttgcttggccttcacttgcggtgtgttgt-----tgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA
 | ||  |  | |||   | |    ||    | || | |  || | ||    |   |  |||||| | ||||   |       |   || | ||| |     |||||| || ||| || |    || || ||||||||||||||||| ||||||||||  || || || | ||| ||| |||||||| ||||  | |||||||||||
-aggc-catccgtagtggatgctgctg---caatgcggt--ttcattgagttgggattatggttcctgttgccgcgatgatgatgatggggggttctgcgtctgcagGAGAAGTCGTTATTTCGCAAGAGCCTTACGCTTCTACACCAAACAAGATTTCTGTGGGCTCCAACTGCGACAATTGTTTCGCCTCCAGAAACCTGAGGAA
















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|211471995|gb|FK962992.1|FK962992
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474518|gb|FK963007.1|FK963007
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211477029|gb|FK963011.1|FK963011
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474509|gb|FK962998.1|FK962998
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474519|gb|FK963008.1|FK963008
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474515|gb|FK963004.1|FK963004
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211471996|gb|FK962993.1|FK962993
EST:     CATCCCCGGNAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474511|gb|FK963000.1|FK963000
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474516|gb|FK963005.1|FK963005
EST:     CATCCCCGGCAAGGGAAGGGGNCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474507|gb|FK962996.1|FK962996
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474508|gb|FK962997.1|FK962997
EST:     CATCCCCGGCAAGGGAAGGGGTCYCATCGCTACTTGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474510|gb|FK962999.1|FK962999
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474520|gb|FK963009.1|FK963009
EST:     CATTCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474517|gb|FK963006.1|FK963006
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474514|gb|FK963003.1|FK963003
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474521|gb|FK963010.1|FK963010
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474512|gb|FK963001.1|FK963001
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211471998|gb|FK962995.1|FK962995
EST:     CATCCCCGGCAA-GGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474513|gb|FK963002.1|FK963002
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccgctgtgttggttcatttgcttggccttcacttgcggtgtgttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA
                ttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacgcataggcatagacacgtccttgaattagtgtgatgatttactgttccgctgtgttggttcatttgcttggccttcacttgcggtgtgttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA

cacgcat
- - - - - - - - - -gtccttg
- - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - tccgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg