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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaagctgcactataatcatggcacacagttacatctactataaccaccatagtgttgtcttcgcatctacataatgtctaacaagttcatcctcag

Basic information

species Oryza sativa
transcript LOC_Os03g63430.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 4
TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaagctgcactataatcatgg-cacacagttacatctactataaccaccatagtgttgtcttc--gcatc-tacataatgtctaacaagttcatcctcag-------------------------
||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| ||| | |||||||||||||| ||||||||||||||||||||||    | ||||||||||   || ||   | || ||| | || | || |   |  |||  |  |   | | | | | | |  ||| || | | |||    |                          
TGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAAAATTAAAGAGGAGCAGGGACAAATTTACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgccccgcactataattgaggacatgtaattccatattctgtgacaatgtttttgtcattctttagtaccgttcctcaattctcacta-tccatgactataatggactaacaagctgtttatcag

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 4
TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaagctgcactataatcatggcacacagttacatctactataaccaccatagtgttgtcttcgcatctacataatgtctaacaagt-tcatcctcag
||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||| ||||||| |||||||||||||| ||||||||||||||||||||||    ||||||| ||   || |   |||  ||| |  |   |  |||  | | ||||    ||     |   || ||| |  ||    |||   ||  
TGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgcactgcactctaga-attgaggacatgtactttcatatt--ccattacaatgtttctgtcattctttagtactgtttctcagtcctcactatcc-

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 4
TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGC------Tgtaagttcaagctgcactata-atcatggcacacagttacatctactata-accacca--tagtg---ttgtcttcgcatctacata-atgtctaacaagttcatcctcag
 || ||||| ||||||||  | |||||||| | ||||||||||||||| || || || ||||  || | ||| ||||||||||| ||||||||| ||||      ||| | ||  |   |    ||  ||  |   |  ||  |     |  | ||   ||| |  |||||   ||  ||     |  || || |||  | |    ||| |   |||
CGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaattttaaacgtgtgatggattttattatgcacctttggtttttgtatgtcactagttagtgaaattagctgtttgttgacttacatgattgat---ttccttaacag

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|86420511|gb|CI056500.1|CI056500
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|29664786|gb|CB661061.1|CB661061
EST:     TTAATGCAAGAAGTTGCT                         G-TGAAACATTNTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCT
genomic: TTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATT-TGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCT
EST: gi|29639942|gb|CB644951.1|CB644951
EST:     GCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: GCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|58681663|gb|CK070350.1|CK070350
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTC
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTC
EST: gi|58685186|gb|CK073873.1|CK073873
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|33812345|gb|CF332062.1|CF332062
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|88265103|gb|CI368877.1|CI368877
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|29664482|gb|CB660757.1|CB660757
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|88210956|gb|CI212596.1|CI212596
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|58694542|gb|CK083229.1|CK083229
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCAT
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCAT
EST: gi|29645308|gb|CB650315.1|CB650315
EST:     AGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GGTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|58681237|gb|CK069924.1|CK069924
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|29645307|gb|CB650314.1|CB650314
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|33795887|gb|CF323811.1|CF323811
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|29658196|gb|CB654471.1|CB654471
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|29664785|gb|CB661060.1|CB661060
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|58659555|gb|CK048235.1|CK048235
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|58593588|gb|CF991896.1|CF991896
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|29639941|gb|CB644950.1|CB644950
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCT
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCT
EST: gi|29678374|gb|CB674649.1|CB674649
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|58678571|gb|CK067258.1|CK067258
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|86495227|gb|CI137860.1|CI137860
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATG
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATG
EST: gi|29637544|gb|CB642553.1|CB642553
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|117217926|gb|CT845200.1|CT845200
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|86534283|gb|CI174489.1|CI174489
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA
EST: gi|19388435|gb|BM929262.1|BM929262
EST:     AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCT                         GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCTTTCATTCTA
genomic: AGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaa ... tcatcctcagGTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaagctgcactataatcatggcacacagttacatctactataaccaccatagtgttgtcttcgcatctacataatgtctaacaagttcatcctcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT