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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgtttatcctttatttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc...

Basic information

species Oryza sativa
transcript LOC_Os04g52900.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GRMZM2G084181_T01 (Zea mays), 5'ss of exon 24
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgtttatcctttattta-----gttca-gaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc
||| ||||||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||||||| || | ||| | |||||||||||| | | |||   |    |||||| |     ||| | ||| |||  ||| |   | | |   |  | ||    || | | ||     ||| ||    | |     
TCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAATTCTTTAGGATTGGATGCTGAGgtatgcaattttcatgat-tttattcatggaagtttacgactattgattctcggctgtcattttattttacaaatg-acacacacacaagtattccactttt----

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GLYMA15G09900.1 (Glycine max), 5'ss of exon 24
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt-tgtttatccttt-atttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtc-agtttttttttgtcagtc
||| || ||||| ||||||||||| || |||||||| || || || ||||| ||| | || ||||| ||| |||||||| || |||| || ||||||||||||  |  |  | |   |  ||| ||  || | |    |||| |     ||  |||| ||||    |   |    | | |  || ||||   |||  |||   
TCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAATTCTTTGGGGCTGGATGCTGAGgtaaatgctaatataggtgttttgatggagatgattgtattaatgagtattggttaaaatgagcattatttactgacattcttctagttgaatttgatca---

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GLYMA13G29180.1 (Glycine max), 5'ss of exon 24
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgtttatcctttatttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc---
||| |||||||| ||||||||||| || |||||||| || || || ||||| ||| | || ||||| ||| |||||||| ||||||| || || |||||||||  |  |     || |   ||  |  || | |  ||   ||| | |      ||    | |  |  | | |    |  | | ||  |||| ||  |||   
TCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAATTCTCTGGGGCTGGACGCTGAGgtaaatgctaatagtaacaagtagatt-ttaaaaatatagcttctcatcccccgagtctttcttgggttatgttatttctttaattaattttggt--gtcata

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 24
lower sequence: AT1G30410.1 (Arabidopsis thaliana), 5'ss of exon 26
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgttt----atcctttatttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc-----------------------------------------
||| |||| ||||||||||||||| |  |||||||| || ||| | || || ||| ||||||||||||| || |||||| || | || |||||||| |||||  ||||||| | |    |  | |  |||| |      | ||   | |      | || || ||  |    |  |||  ||      ||||||||| | | |                                          
TCCATTTAGTGAGCACAATGATGCTGGCCTCTGGGAGGCTCTTCACAGAGCGCATATAAAAGATGTCATCAGCAGGAATCCTTTTGGCCTAGATGCAGAGgt--gtagtttatcttaaaagacatagtttaatcagattctttcagttatacgcataaaaataatccacttttagataatctcaatc-tttttttttatgattgagattattgattaaactctcacccactttgagtctgtgaag

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 24
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 5'ss of exon 24
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgttta-tcctttat-ttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc
||| |||| ||| ||||||||||| || |||||||| || || |||||||| ||| |||||||||||||    |||||| || | || |||||||| ||||||     | | |||| |    ||| ||||||   |  ||| ||| |  ||| ||| |  ||||  ||     ||  |  ||| |  |||  | ||| |   
TCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAATCCTTTTGGCCTAGATGCAGAGgtatagtttatctttagtgacatatattagttagaagaattctttga--tttcttatggagatggctg-----atcaaagtgtta-ctttaatctgtaaag-

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 24
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 24
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgtttatcctttatttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc--
|||||| || |||||||||||||| || |||||||| ||  | || ||||| ||| | || ||||| || ||||||||| |||| || || ||||||||||||| |  |    ||  | ||  |  |          || | ||||| | |||    |  | | |   |  |    | ||    | ||   |||||| |   
TCCTTTCAACGAGCACAATGATGCTGACCTCTGGGAGGCTTTAGAGAGGGCACATTTGAAGGATGTTATCAGGAGGAATTCTCTTGGTCTTGATGCTGAGgtacatgctcaaatttgctttagtagatcattattttttttctcactctctttttctttttctctttttcaaacagcatg--gatattaaattgtcaattga

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|33381540|gb|CF196883.1|CF196883
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58691149|gb|CK079836.1|CK079836
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58655688|gb|CK044368.1|CK044368
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|33380305|gb|CF195648.1|CF195648
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58690744|gb|CK079431.1|CK079431
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAG
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAG
EST: gi|25804050|gb|CA760011.1|CA760011
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58693939|gb|CK082626.1|CK082626
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTAGTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58658993|gb|CK047673.1|CK047673
EST:     CTCATCTAAAAGATGTCGTAAGGAGGAATGCTCTGGGACTA-ATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|29671480|gb|CB667755.1|CB667755
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|33380452|gb|CF195795.1|CF195795
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|33380456|gb|CF195799.1|CF195799
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|33380394|gb|CF195737.1|CF195737
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58588567|gb|CF986875.1|CF986875
EST:     CTCATCTAAAAGATGCCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|58657519|gb|CK046199.1|CK046199
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|112786349|gb|EE590578.1|EE590578
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|66919516|gb|CX106364.1|CX106364
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
EST: gi|84117316|gb|CD151083.1|CD151083
EST:     CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAG                         GTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT
genomic: CTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtt ... acacactcagGTCTCTGAGGCTGGTGAAAATTTTAGCGTTGGACAGCGGCAGCTACTGAGT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAATGCTCTGGGACTAGATGCTGAGgtacgtagtttgtttatcctttatttagttcagaccattatttcactttttttaagatgatgtatgcctgtatagacttgtcagtttttttttgtcagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG