Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccgcccgcccctccctctctctccactgctaatgtcccttctcctctctctctctctctctctgctgtgccctgatctgacgtttcctttgcttggatctggcgcggcag

Basic information

species Zea mays
transcript GRMZM2G113016_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113016_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g49040.1 (Oryza sativa), 5'ss of exon 1
CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccgcccgcccctccctctctctccactgctaatgtcccttctcctctctctctctctctctctgctgtgccctg-atctgacgtttcctttgcttggatctggcgcggcag
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |  | || ||||| || ||||| |||     |  |  ||     ||    ||||| |       | | |||        |||   |||    ||    || ||| ||| | |  |  |||||||||  |    |||  |||
CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcctcttccttgatctactactccattttattcattcattcattcactactcctcctcatcatgtcacgcgctggatccgtccgt--ctttgcttgcttgcttcgcctcag
















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|71322508|gb|DR797928.1|DR797928
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483137|gb|FK978314.1|FK978314
EST:     ACTGCCTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|149082616|gb|EE171816.2|EE171816
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211480254|gb|FK978308.1|FK978308
EST:     ACTGCCTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|101394213|gb|EB819041.1|EB819041
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483138|gb|FK978315.1|FK978315
EST:     ACTGCCTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCCGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|89251895|gb|DY623681.1|DY623681
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211480255|gb|FK978309.1|FK978309
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|148943771|gb|EC888842.2|EC888842
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211480257|gb|FK978311.1|FK978311
EST:     ACTGCCTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|71425430|gb|DR806665.1|DR806665
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|50336767|gb|CO531893.1|CO531893
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483144|gb|FK978321.1|FK978321
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|148999591|gb|EE036571.2|EE036571
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|149109868|gb|EE293669.2|EE293669
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|148933045|gb|EE285941.2|EE285941
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211486018|gb|FK978327.1|FK978327
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483148|gb|FK978325.1|FK978325
EST:     ACTGCCTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483149|gb|FK978326.1|FK978326
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211480250|gb|FK978304.1|FK978304
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCG
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCG
EST: gi|211480258|gb|FK978312.1|FK978312
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211480251|gb|FK978305.1|FK978305
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|148932896|gb|EE285678.2|EE285678
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483145|gb|FK978322.1|FK978322
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|93284247|gb|EB676511.1|EB676511
EST:     ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
EST: gi|211483139|gb|FK978316.1|FK978316
EST:     ACTGCCTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCC                         GTGTTCCACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT
genomic: ACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCAT

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), 48 (downstream exon)
Score: 36

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCATCTGCTCGAGCACGTCATGAGCGCGCTGCCGCCGGACATCGGGCGCGACG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 30

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCATCTGCTCGAGCACGTCATGAGCGCGCTGCCGCCGGACATCGGGCGCGACG


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 21

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCATCTGCTCGAGCACGTCATGAGCGCGCTGCCGCCGGACATCGGGCGCGACG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 29

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccg ... ggcgcggcagGTGTTCGACGGCCACAACGGCGTGTCGGCGGCGGTCTATAGCAAAGAGCATCTGCTCGAGCACGTCATGAGCGCGCTGCCGCCGGACATCGGGCGCGACG