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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_T01
intron # 3
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|211474515|gb|FK963004.1|FK963004
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474521|gb|FK963010.1|FK963010
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211477029|gb|FK963011.1|FK963011
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474511|gb|FK963000.1|FK963000
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|149023564|gb|EE045895.2|EE045895
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474516|gb|FK963005.1|FK963005
EST:     CATCCCCGGCAAGGGAAGGGGNCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474513|gb|FK963002.1|FK963002
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474517|gb|FK963006.1|FK963006
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474510|gb|FK962999.1|FK962999
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211471995|gb|FK962992.1|FK962992
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474507|gb|FK962996.1|FK962996
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211471996|gb|FK962993.1|FK962993
EST:     CATCCCCGGNAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474508|gb|FK962997.1|FK962997
EST:     CATCCCCGGCAAGGGAAGGGGTCYCATCGCTACTTGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474518|gb|FK963007.1|FK963007
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|71322965|gb|DR798157.1|DR798157
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474514|gb|FK963003.1|FK963003
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474519|gb|FK963008.1|FK963008
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474512|gb|FK963001.1|FK963001
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTCGCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211474509|gb|FK962998.1|FK962998
EST:     CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
EST: gi|211471998|gb|FK962995.1|FK962995
EST:     CATCCCCGGCAA-GGAAGGGGTCTCATCGCTACTTTCACCTTCTTCCCAG                         GGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT
genomic: CATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 47

TTGGAGCAGCTGCAGCGCGAGCTCGCCGCCCGCGGCCTCACAGTCGCCTCCATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 24

TTGGAGCAGCTGCAGCGCGAGCTCGCCGCCCGCGGCCTCACAGTCGCCTCCATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 11

TTGGAGCAGCTGCAGCGCGAGCTCGCCGCCCGCGGCCTCACAGTCGCCTCCATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 17

TTGGAGCAGCTGCAGCGCGAGCTCGCCGCCCGCGGCCTCACAGTCGCCTCCATCCCCGGCAAGGGAAGGGGTCTCATCGCTACTTGCACCTTCTTCCCAGgtgaaaccgc ... gttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccgctgtgttggttcatttgcttggccttcacttgcggtgtgttgttgcagGGGATGTCATTCTCAATCAGGAACCTTACGCTTCTACACCTAACAAGATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAA
                ttcattt  TA-rich tract