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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcctttccacccacaaagcgtgaaatgtgaaagggtagtagtaggaccatgagcagacatatttctacttagtactttcttccttagtcatata...

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132060_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G07760.1 (Glycine max), 5'ss of exon 7
GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcctttccacccacaaagcgtgaaatgtgaaagggtagtagtaggaccatgag-cagacatatttctact-----tagtactt-tcttccttagtcatata
||||||||||||||||||||||| |||||| ||||||| || ||  | ||||| ||||| || || ||||| |||||||||||||||||||||||    |   |      ||| |   |       ||   || |  | ||     || | | ||||  |||||  |       || || || | || ||| ||      
GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttgtgttttgcaccatttgcattgcttgcttggttttttgtttactcaagtgtcagaactattttcatcctttctaatagttctttttcttggttgctag

upper sequence: GRMZM2G132060_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G31550.2 (Glycine max), 5'ss of exon 7
GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagact---------cctttccacccacaaagcgtgaaatg--tgaaagggtagtagtaggaccatgagcagacatatttctacttagtactttcttccttagtcatata
||||||||||||||||||||||| |||||| ||||||| || ||  | ||||| ||||| || || ||||| |||||||||||||||||||||||    |         |||||       ||     || | ||  ||   || |  |  |    | |    ||||  ||||   |        | | ||  || ||      
GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAGgtttcatttgtgtttgcctttggttttgcaccatttgcattgcttgcttggtttttgtttactctagtttcagaactattctcatccttagttctttttattggttgccag

upper sequence: GRMZM2G132060_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcctttc-cacccacaa--agcgtgaaatgtgaaagggtagtagtaggaccatgagcagacatatttctacttagtactttcttccttagtcata-ta----------------------------------
||||||||||| || || || ||||||||| | || || || ||| | ||    |||||||| |||||||| || ||||| |||||||||||||||   | |||   |   |  ||     ||| ||   | | || |  |  | ||  |||  |      ||  || |  |||    |        ||||  | ||                                  
GCTTATATTGAAAAGGAAGACAGCAAGAAGCTTAAGCAAAAGCAGAGGGAAAAGATGCAGCCAAAGATGGGGAAGATGGACATAGATTATCAGgtaatgtgcttaagctttcggaattgatgtggaaatgggatggctcttgtttggtgcattcgtcc-tttacatcaaagtagagtatatccagagagtcgaagtagttggtgtttaagtttatgtcctgtactttgcag

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|31359279|gb|CD443636.1|CD443636
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT
EST: gi|13382081|gb|BG458756.1|BG458756
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCGTTCTTCAAATATCACACAAAACCCAAGCTGTCTAGT
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT
EST: gi|148931686|gb|EC874876.2|EC874876
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGA
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGA
EST: gi|13382209|gb|BG458884.1|BG458884
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCGTCTCTTCAAATATCAGACAAAACCCAAGCTGTCTAG
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGT-TCTTCAAATATCAGACAAAACCCAAGCTGTCTAG
EST: gi|21843267|gb|BQ703848.1|BQ703848
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT
EST: gi|148931684|gb|EC874873.2|EC874873
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCG
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCG
EST: gi|26557871|gb|CA830106.1|CA830106
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTC
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTC
EST: gi|148966452|gb|EE017460.2|EE017460
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GTTTTGCATGACGCGTTCTTCAAATATCAGAACAAA-CCCAAGCTGTCTAG
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGA-CAAAACCCAAGCTGTCTAG
EST: gi|21843287|gb|BQ703868.1|BQ703868
EST:     AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG                         GGTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT
genomic: AGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGT

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: 49 (upstream exon), 49 (downstream exon)
Score: 523

GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 379

GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcct ... ttcttggcagGTTTTGCATGACGCGTTCTTCAAATATCAGACAAAACCCAAGCTGTCTAGTCATGGTGATCTGTATTATGAAGGCAAAGAATTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAGgtagactcctttccacccacaaagcgtgaaatgtgaaagggtagtagtaggaccatgagcagacatatttctacttagtactttcttccttagtcatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacccac