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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
gtattatttgacctagcgggca-actgatgagattcact--------tgtg--tctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
|||| ||   | | |        | | ||||| |  ||         ||||  ||||||  ||||    || ||  | ||||||||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| || ||||||
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 5
---------gtattatttgacctagc---gggcaactgatgagattcacttgtgtctcaagccta-accagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
         |  | | | |   ||       |   ||| |   | | | ||||   |     ||       |    | |||   |||||||||||||||| || || |||||||| || |||||||| || || || |||||||| || || || || |||||| | || || 
gttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
-------------gtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
                ||| ||    | | ||   | |     | |   |||  ||  ||||   ||    |||||   ||  || ||||||||||||||||| ||||||||||| || ||||| || || ||||| || ||||| || || |||||||| ||| | || |||
gtattaatgttgtaagttacttttttttgtggtgtatttccttg-tatgcttcagtgacaagaaaaat--atggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 18
---------------------gtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
                     || |   |||| ||  |       | || || ||    ||  | ||||  |       ||   |  ||   ||||||||||||| || || ||||| ||||| || ||||||||||| || || ||||||||  | || |||||||||||| | ||||||
gttaaatttgtccctctccaagtgtatattgatctcacc-----tttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
----gtattatttgacctagcgggca-actgatgaga--ttcacttgtgtctcaagccta--accagt------ggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
       || | |  |     | | | | ||||   |  || | | || |     || ||  ||   |      |  || |||   |||||||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||  | || |||||||||||| | ||||||
gttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
gtattatttgacctag-cgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
|||||  |      |  |||  | ||||    ||    || | | | |      ||  |   |  | || | |  ||||||||||||| || |||||||| || || |||||||||||  |||||||||| ||||| || || || || ||| | ||||||
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
gtat-tatttg-acctagcgggcaactgatgagat-tcacttg-------tgtctcaagcctaaccagtggttcgtt--tactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
|||  ||| || | | |   ||  |||    || | ||  |||       ||| |  |   ||           | |  | ||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||||| |||||||| || || |||||| | ||| | || |||
gtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG

upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 22
----------------------------gtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
                             |||   |||| ||     |    |  ||  |||   || | |||||   ||      |  |   | |  || ||||||||||| || || ||||||||||| ||||| ||||||||||| || |||||||| || || |||||| ||||| | ||||| 
gttatcattgataagtagcttcttttttctatcccttgatctctatagtgggt--tgttatttttttttttctcag--ctggtttctcatctttcttgttgcagTGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAA

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|22490580|gb|BU050503.1|BU050503
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|67025653|gb|CO454402.1|CO454402
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|87153787|gb|DY398576.1|DY398576
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|67034427|gb|CO462977.1|CO462977
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGGGTTGGT-AANGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAA
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGT-TTGGTGAA-GGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAA
EST: gi|22490811|gb|BU050734.1|BU050734
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|87152067|gb|DY396856.1|DY396856
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|19058833|gb|BM737500.1|BM737500
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|19058784|gb|BM737451.1|BM737451
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|211048836|gb|FL187596.1|FL187596
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT

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: 130

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 186

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
                           gcctaac  putative branch site (score: 186)
                                            tttactttc  putative PPT
                                            tttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG

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