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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattccaataatgtggagtctagtggatatggcctagtgcacttcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC

Basic information

species Zea mays
transcript GRMZM2G107867_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 10
tatattccaat---aatgtggagtctagtggatatggcctagtgcacttcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC
|||| |   ||   ||||| |   ||  || || |||  | ||    |  | |||     | ||||||  |  | |||||||    ||||   | ||  ||||||||||||||| |  ||||| ||||| ||  | ||||||||||||||||| || |||||||| || ||||| ||||||||||| | ||||||||||||||
tatagtatcattcgaatgttgtagctgttgtatttggtat-gtattatatatatgttgtatatctggctgtagaattgctgattccgtttc--ttttcttcagCTTTACAAGACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGACTTCCTTACCAAGC

upper sequence: GRMZM2G107867_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g17980.1 (Oryza sativa), 3'ss of exon 10
tatattccaataatgtggagtctagtggatatggcctagtgcacttcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC---------
   |||| |||  ||| |   ||  || || |||  | ||    |  | |||     | ||||||  |  | |||||||    ||||   | ||  ||||||||||||||| |  ||||| ||||| ||  | ||||||||||||||||| || |||||||| || ||||| ||||||||||| | ||||||||||||||         
---attcgaatgttgtag---ctgttgtatttggtat-gtattatatatatgttgtatatctggctgtagaattgctgattccgtttc--ttttcttcagctttacaagACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGACTTCCTTACCAAGCTGAGGGTTC

upper sequence: GRMZM2G107867_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 10
-----tat-attccaataatgtggagtctagtggatatggcctagtgcacttcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC
     ||| |||| |||  ||| |   ||  || || |||  | ||    |  |  |      | ||||||  |  | || ||||    ||||   | ||  ||||||||||||||  |  ||||| ||||| ||  | ||||||||||||||||| || |||||||| || ||||| ||||||||||| |||||||||||||| |
tatagtatcattcgaatggtgtag---ctgttgtatttggtat-gtattatatattttttgtatatctggctgtcgaattactgattccgtttc--ttttcttcagCTTTACAAGAGCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGCCTTCCTTACCAAAC

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|5361136|gb|AI795751.1|AI795751
EST:     ATGATGATGCAAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCCTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|211186172|gb|FL452293.1|FL452293
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|60341419|gb|DN208392.1|DN208392
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGA
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGA
EST: gi|71762342|gb|DR960279.1|DR960279
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|91872727|gb|EB402684.1|EB402684
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTAC
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTT-ACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTAC
EST: gi|5871760|gb|AW018231.1|AW018231
EST:     ATGATGATGCAAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCCTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|60345406|gb|DN212379.1|DN212379
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|6056642|gb|AW091047.1|AW091047
EST:     ATGATGATGCAAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCCTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|108954035|gb|EC364982.1|EC364982
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|5108343|gb|AI740056.1|AI740056
EST:     ATGATGATGCAAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCCTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|211186173|gb|FL452294.1|FL452294
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|60398350|gb|DN231166.1|DN231166
EST:     ATGATGATGCAAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCCTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|110532366|gb|EE036550.1|EE036550
EST:     ATGATGATGCTAATGGGAGGCTACCTCCTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|71758603|gb|DR956540.1|DR956540
EST:     ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT
EST: gi|78021650|gb|DV490037.1|DV490037
EST:     ATGATGATGCAAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAG                         CTTTACAAGACGAAGGACGACAAGTACCTCCTAGATATGCAGAGAGTTACT
genomic: ATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagta ... tctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC
                            tgctgac  putative branch site (score: 2)
                                    ttgttttattctttct  CT-rich tract
                                   attgttttattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatattccaataatgtggagtctagtggatatggcctagtgcacttcaaatgcctattctctggcgctgcatttgctgacattgttttattctttctcagCTTTACAAGACGAAGGACGACAAGTACCTCTTAGATATGCAGAGAGTTACTGGACCTCAGCTGCTCTTCCTTGACTTCTGTGCGGCCTTCCTTACCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT