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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaccgagaataccatttacacagtcgaaagtgaaaagtgatcaaaccggtgtcctcttgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA

Basic information

species Zea mays
transcript GRMZM2G175071_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g16350.1 (Oryza sativa), 3'ss of exon 7
-------------gtaac-aaaccgagaataccattta--cacagtcgaaagtg--aaaagtgatcaaaccggtg---------tcctcttgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA
             ||  | |        || ||||||      | | |||| ||    |||   ||  |||   |         |   | | | || |||||||| || ||||| |||||||| ||||| || |||||||| || ||||| |||||||| ||||| ||||| |||||||||||||||||||| |||||||
acctccgagtgcagtggccaggatatttattccattttgttctactggaaaatgctgcaagctttcttaccaacgattactgcatttgcctttgaatcagATGGGTGTGAGCGTTGTGGACTCTTCCGTAGCGGGCCTCGGAGGGTGCCCATACGCGAAAGGTGCATCGGGCAATGTGGCGACGGAGGACGTGGTGTACA

upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ15246 (Selaginella moellendorffii), 3'ss of exon 5
----gtaacaaaccgagaat--accatttacacagtcgaaagtgaaaagtgatcaaaccggtgtcctcttgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA
    || |  ||   |   |   |  ||| | |  |       ||  || ||   | |   |||    ||||     |||||||||| |||   ||||| || |||||  | || |||||||||||||| |||||||| || ||||| ||||| || ||||||||||||||  | ||  
gtgagtgatcaattcactcttcgcttttttctcgtttcttctcgagtagggaatgagctc-tgtggatttgtt--ttagATGGGAGTGAGCACCGTGGATTCGTCCGTGTCAGGGCTCGGTGGCTGCCCCTACGCGAAAGGCGCGTCTGGGAACGTAGCGACGGAGGACGTGATCTATC

upper sequence: GRMZM2G175071_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ08384 (Selaginella moellendorffii), 3'ss of exon 5
----gtaacaaaccgagaataccatttacacagtcgaaagtgaaaagtgatcaaaccggtgtcctcttgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA
    || |  ||   |   | |  |||     ||      |    | ||| |     ||  |  | ||       |||||||||| |||   ||||| || |||||  | || |||||||||||||| |||||||| || || || ||||| || ||||||||||||||  | ||  
gtgagtgatcaatttactcttcgttttttctcgtttcttctagggaatgagctctgtggatttgtttt-------agATGGGAGTGAGCACCGTGGATTCGTCCGTGTCAGGGCTCGGTGGCTGCCCCTACGCGAAAGGCGCCTCTGGGAACGTAGCGACGGAGGACGTGATCTATC

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|149010240|gb|EE042062.2|EE042062
EST:     TCCACGACACCTACGGCCAGTCCCTTTCGAACATTTTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGGCTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|94478825|gb|EB707783.1|EB707783
EST:     CGGCCAGTCCCTCTTGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCTCCGGCCTCGGTGGCTGCCCG
genomic: CGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|148975812|gb|EE025802.2|EE025802
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|76013105|gb|DT940275.1|DT940275
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|60394740|gb|DN227610.1|DN227610
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|71430394|gb|DR811444.1|DR811444
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|71772252|gb|DR970189.1|DR970189
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|74240107|gb|DT648021.1|DT648021
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|86467648|gb|DY234018.1|DY234018
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|149064134|gb|EE286430.2|EE286430
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|60356988|gb|DN223961.1|DN223961
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|60351778|gb|DN218751.1|DN218751
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|37382455|gb|CF628174.1|CF628174
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|74237798|gb|DT645712.1|DT645712
EST:     ACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: ACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
EST: gi|76293871|gb|DV033439.1|DV033439
EST:     TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAG                         ATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG
genomic: TCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCG

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: 43 (upstream exon), 47 (downstream exon)
Score: 39

GCTTGAGGCAGCTATCTCCGTCGTTCCCGTGGAGAAGCTCGCTGTCCACTTCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 54

GCTTGAGGCAGCTATCTCCGTCGTTCCCGTGGAGAAGCTCGCTGTCCACTTCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 59

GCTTGAGGCAGCTATCTCCGTCGTTCCCGTGGAGAAGCTCGCTGTCCACTTCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 16

GCTTGAGGCAGCTATCTCCGTCGTTCCCGTGGAGAAGCTCGCTGTCCACTTCCACGACACCTACGGCCAGTCCCTCTCGAACATTCTCATCTCTCTTCAGgtaacaaacc ... tgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttacacagtcgaaagtgaaaagtgatcaaaccggtgtcctcttgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA
                                       tcctcttgtc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaccgagaataccatttacacagtcgaaagtgaaaagtgatcaaaccggtgtcctcttgtcaaccagATGGGAGTAAGCGTGGTGGACTCCTCCGTCGCCGGCCTCGGTGGCTGCCCGTACGCGAAGGGTGCGTCGGGGAATGTGGCGACGGAGGACGTAGTGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA