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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctcatcatttatgatgtttctgttatcatttttctttcatgctttatgaacctttttgtccctgttgcag

Basic information

species Zea mays
transcript GRMZM2G079256_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 5'ss of exon 5
GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctcatcatttatgatgtttctgttatcatttttctttcatgctttatgaacctttttgtccctgttgcag
||| |||||||||||||||||||||||| | ||||| || ||| |||| ||||||| |||| | ||||||||||||||||| ||||||||| |||||||||    | ||  ||| | |    | || |  ||  || |||| |  |    | ||| || ||
GCTTCCTGATGGATCTCTTATGGAGATTACAAAAGTCTACCCATTGGATGCAGTTTTTGACTCTCCTGAGGATGTTCCTGATGATgtaatgttcatcattttcttttttcatgtcaac----tcctgttctgtattctgaatcggtc---ctctggtgtag

upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G31780.1 (Glycine max), 5'ss of exon 4
GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctcatcatttatgatgtttctgttatcat------ttttctttcatgctttatgaacctttttgtccctgttgcag----------
  |||  ||||| ||  | ||||||||||||||||| |||||  |||| ||||| |||||||  ||||| ||||| || |||||||||| |       |  || ||  || ||  |  |       |    || ||    || | | | | | | |   ||||| |           
ATTACAAGATGGTTCGTTAATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAATCCTGAAGATGTCCCGGAAGATgtaa-gagagaagtacataatagttatgaaaatacacaacgtacatttacaaaacttttcatcttctatttttttgttgaaaaattgtatag

upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 6
GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaa-tgctcatcatttatgatgtttctgt-tatca----tttttctttcatgctttatgaacctttttgtccctgt-tgcag
  |||| ||||| ||  | ||||||||| | ||||| |||||| |||| ||||||| |||||  || || ||||| |||||||||||||   |        ||   | ||| ||  | |||    || |    |||||||   |     ||||||  |   | |  ||
ATTACCAGATGGCTCGATGATGGAGATTACCAAAGTTTATCCATTGGATGCAGTTTTTGACAATCCCGATGATGTGCCTGAAGATgtaaacacgagatgcctaatttctttttgcatgtcagaacttatatcctcatgctgattttttttttttggacaattatatag

upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G45990.1 (Glycine max), 5'ss of exon 5
GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctcatcatttatgatgtttctgttatcat------ttttctttcatgctttatgaacctttttgtccctgttgcag----------
  |||  ||||| ||  | ||||||||||||||||| |||||  |||| ||||| |||||||  ||||| ||||| || |||||||||| |       |  || ||  || |   |  ||      |    || ||    |||| | | ||| | |   || || |           
ATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGATgtaa-gagagaagtacataataattatcaaaatatacaaagtacatttacaaaacttatcatcttttatttttttggtggaaaattgtatag

upper sequence: GRMZM2G079256_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 5'ss of exon 5
GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaat------gctcatcatt-tatgatgtttctgttatcatttttctttcatgctttatgaacctttttgtccctgttgcag----
| | || ||||| ||| | ||||||||  | ||| |||||||  |||| |||||||||||||||| ||||||||| |||||||||||||       | | ||  |  ||| ||   | ||  |     |    | ||| ||   |  | | || | |      |  |     
GTTGCCAGATGGTTCTTTGATGGAGATCACCAAAATATATCCTTTGGATGCAGTTTATGACACCCTTGAGGATGTACCTGAAGATgtaagaaagaagtttattgtcctataataaatatgaaaaatggtcaagtgcatcctcagtatatcattgttttatgagtctatgcag

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|60345537|gb|DN212510.1|DN212510
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|32907240|gb|CF012053.1|CF012053
EST:     ATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCCTGA-GAT                         GTTAAAGCACACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAA
genomic: ATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCC-TGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|78076466|gb|DV504900.1|DV504900
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|32908286|gb|CF013099.1|CF013099
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|67011703|gb|CO440452.1|CO440452
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|87156317|gb|DY401106.1|DY401106
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|32911684|gb|CF016496.1|CF016496
EST:     TATATCCACTGTACGCAGGTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GCTAAAGCAAACAAAAGATATGCTGGNAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGG-AGCTTCAAACTGGACTGTTAAG
EST: gi|71332949|gb|DR803501.1|DR803501
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|211314447|gb|FL116841.1|FL116841
EST:     ATCCACTGGGACGCAGTTTATGACACCCCCTGAAGAATGTCCCTGAAGAT                         GTTAAAGCAAACNAAAAGAAATGCTGGGAGCTTCAAACTGGACCTGGTTAA
genomic: ATCCACTGG-ACGCAGTTTATGACACCCC-TGAGGA-TGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAAC-AAAAGATATGCTGG-AGCTTCAAACTGGAC-TG-TTAA
EST: gi|22819573|gb|BU499663.1|BU499663
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|31356068|gb|CD440425.1|CD440425
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG
EST: gi|211312415|gb|FL116823.1|FL116823
EST:     TATCCACTGGACGCAGTTTATGACACCCCCTGAAGATGTTCCNTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGA-TGTTTAAA
genomic: TATCCACTGGACGCAGTTTATGACACCCC-TGAGGATGTTCC-TGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTT-AAG
EST: gi|26559923|gb|CA832158.1|CA832158
EST:     TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT                         GTTAAAGCAAACAAAAGATATGCTGGAGC
genomic: TATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGC

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: 46 (upstream exon), 49 (downstream exon)
Score: 235

GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 222

GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 114

GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctca ... cctgttgcagGTTAAAGCAAACAAAAGATATGCTGGAGCTTCAAACTGGACTGTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGATgtaatgctcatcatttatgatgtttctgttatcatttttctttcatgctttatgaacctttttgtccctgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA