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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

Basic information

species Zea mays
transcript GRMZM2G126453_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
gtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
|||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  |||||||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 5
---------gtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaac------tttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
         |  | | |     || |          ||  ||    || |   |||    | | | ||| | | ||  |       |||||||||||||||| || || |||||||| || |||||||| || || || |||||||| || || || || |||||| |||| || 
gttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcat--tttatctgtgttcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
-------------gtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                ||| ||    |  |||   | |     | |   || | ||  ||||   ||    ||||||  |   || ||||||||||||||||| ||||||||||| || ||||| || || ||||| || ||||| || || |||||||| ||| |||| |||
gtattaatgttgtaagttacttttttttgtggtgtatttccttg-tatgcttcagtgacaagaaaaat--atggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 18
----gtattatttcacctaatgggca-actgatgaga--ttcactactgtctcaaggctaaccagtggtttgttaact---------ttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
       || |  | |   | | | | | ||||   |  || | || | |     |  || | | |  | |  |  |          ||||||||||||| || || ||||| ||||| || ||||||||||| || || ||||||||  |||| |||||||||||| ||||||||
gttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
----gtattatttcacctaatgggca-actgatgaga--ttcactactgtctcaaggctaaccagtggtttgttaact--------ttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
       || | || |   | | | | | ||||   |  || | || | |     |  ||        ||| ||  ||        |||||||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||  |||| |||||||||||| ||||||||
gttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
gtatt-atttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
||||| ||  |    || ||  | ||||    ||    |  | | | |      ||  |   |  | |  | |  ||||||||||||| || |||||||| || || |||||||||||  |||||||||| ||||| || || || || ||| ||||||||
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
----------gtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgtta--actttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
          | || |        | |  ||| ||          | |  ||| |  |   ||          || ||   ||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||||| |||||||| ||||| |||||| | ||| |||| |||
gtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 22
-----------------------gtattatttcacctaatgggca-actgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                        | || | || | | ||    | | ||    | |    |  | | ||   |||      |  | | |    || ||||||||||| || || ||||||||||| ||||| ||||||||||| || |||||||| || || |||||| ||||| | ||||| 
gttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAA

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|58029637|gb|CX725064.1|CX725064
EST:     AAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|32934898|gb|CF039710.1|CF039710
EST:     AAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCTAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT

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), 46 (downstream exon)
Score: 279

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 239

CGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAGgtattatttc ... taactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
                                          tgttaac  putative branch site (score: 239)
                                                ctttc  CT-rich tract
                                        tttgttaa  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG