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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA

Basic information

species Zea mays
transcript GRMZM2G122135_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 5
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                   || |||    ||| |||      | |  |  || | |    |||    ||   |     ||| |  || | |    |||  ||| | | |   |   | || || |  | ||| | || ||||| ||||| ||||| ||  | ||||| ||||||||||||||||| || ||||| |||||||||||||| || ||||| ||||| || |||
-------------------aaatcatgtgatttttg------tattgattatctcttatgattaccaaggccc-----aactctgaagcctaagcaatatatttatttttcttaactattgtttgtgt-agAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGTGATAATGAGGCTGAAGTACGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                 ||| ||||  ||| | |      | | ||  |||      ||| || | | ||||  |||   | || |     ||||| | || |   | ||||    || |        |||  | || ||||| ||||||||||||||||| || || ||||||||||||||||| || || || |||||||| |||||||||||||| | |||||| |||
-----------------tgacttcatactaatttcttcttggtctatgaca------tgatttatagtgtatt-tgttt-ctcaca-----ttctagttgactgtttatataatggtgatgc-acttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 5
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtt-tttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                      | | | | | |||   |  |||   |  || | |    |||  | ||   |     ||| |  || | |    |||  ||| | | |   |   | || |||  ||  ||| | || ||||| ||||| ||||| ||  | ||||| |||||||||||||||||||| ||||| |||||||||||||| || ||||| ||||| || |||
----------------------taatcatgtgatttttgtattg---attatctcttatgattactaaggccc-----aactctgaagcctaagcaatatatttatttttcttaactattgtttatga--agAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGAGATAATGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 5
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                 ||| ||||   || | |      | | ||  |||||  |   | | | |   | ||    |  |  ||   |||||   |||          ||    |||   |||     ||| | || ||||| ||||||||||||||||| || || ||||||||||||||||| || || || |||||||| |||||||||||||| | ||||||||||
-----------------tgacttcatattaatttcttcttggtctatgacatgatttatagtgtatttatttctcacattctaattgactttttatatg----------atggtgatgcacttg----cagATCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATATTA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                            |||| ||    | |  || || |    ||     |    |||   ||||     |||     ||| || |   || ||   || | | |  |  |     |||  | |||||||| || ||||||||  |  | ||  | || ||||||||||||||||||||||| || || |||||||| || |||||||| ||  | || 
------------------------tctttattctttttcgttcatataagagccttccatggt----agttctatgtttgtacatgtatctttttatt---ttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------gtattatttgtgctagctgaattcaacctatt-attgcagggttgtaaaacat---gtatctgaa--tttttgagtatcatgtaaaccca-taaccttttctaatggattaactgtatatc----tatgtttttgggattagAG-CTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                                                ||   | ||| |    |  |||| | ||  ||| | |  ||   |   ||   |||  || |  |   ||  | |   || | |  | |||  || | | |    ||   | ||  |     | ||  ||  | ||||  | | ||| ||||||||||||||| |||||| ||| | ||||||||||| ||||| || ||||| |||||||||||||| || ||||| || ||||| |||
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAG-CTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                                     || ||  | || | |   |||| ||  | | | |  ||   || | | |||  |   |  ||   ||   | |||  | |||||   |||      | |||  ||| | || || ||| ||     |||  | | ||  |||||||||||||||| || || ||||| |||||||| |||||||| || ||||| ||||| |||||||| || ||||| || || ||  ||
gtaagaacgttttgcataaacctaatgcagcatgttttaatacctttgatgggctaatttaatgt-tcaatatagaaatgcatatcatccaataggcttaaggaacttgatg--atcccatttacttcctc--ttgat--actattta-ctgtgtcttctattttaagGACGGAGCTGGTGCCTGCATATGTGCGCCTACTTCGTGATAATGAAGCTGAAGTACGCATAGCAGCTGCCGGAAAAGTTACAAAGTTTTGTCGGATTCTA

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 6
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                            | ||      || || |     || | | |  |||||| |  |   | |  |   | |   || | | |   || |    ||  | | || | ||  |   ||  | || ||||| ||||||||||||||  | ||||| || |||||||||||||| || ||||| ||||| ||||||||||| || || ||||| || || 
----------------------------tttttggattggtttattcctgatctgtgtccattttttaacaaattatttatata-attgttatttgacttatgattgataattatttgatattttg--cagGTCAGACTTGGTTCCTGCATATGTTCGGTTGCTTCGTGACAATGAGGCTGAAGTACGCATAGCAGCTGCAGGAAAAGTAACAAAATTTTGCCGGATTTTG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatcta-tgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                              | ||  || | ||      |   |||||  ||||       |  | |    |  |    |||| |  |   ||   | | |    | || | |     | ||| | || ||||| || || ||| | ||  | ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||| ||||| |  || |||
------------------------------taatctcaagttttcctggct--tatcttgatttcctttctttctttctttctttctttttttttttttttttttttttgtggtgactgatatcattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTA

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|32929087|gb|CF033899.1|CF033899
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|6564198|gb|AW231820.1|AW231820
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|31356310|gb|CD440667.1|CD440667
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|5566949|gb|AI881860.1|AI881860
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|67034361|gb|CO462911.1|CO462911
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|24763712|gb|CA398883.1|CA398883
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|13126723|gb|BG317293.1|BG317293
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGT
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGT
EST: gi|20803006|gb|BQ294056.1|BQ294056
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|32941448|gb|CF046267.1|CF046267
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|13126316|gb|BG316886.1|BG316886
EST:     GCCAATCAGCTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATA
EST: gi|211221964|gb|FL414368.1|FL414368
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|32928593|gb|CF033405.1|CF033405
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
EST: gi|31361222|gb|CD445579.1|CD445579
EST:     GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG                         AGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA
genomic: GCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAGgtattatttg ... ttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
                       gattaac  putative branch site (score: 2)
                                        tgttttt  putative PPT
                                tatatctatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA