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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgaatatacttgtgtttttgttatttctgcacactatttcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG

Basic information

species Oryza sativa
transcript LOC_Os01g57220.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 7
gttgtgaatatacttgtgtttttgttatttctgcacactatt--------tcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
||||||  |||  || || | |   ||||  |||||| |            | || |  |||| ||||  ||| || ||  ||||| | || ||||||||| ||||||||||||||||| ||||||||| |||||||| | 
gttgtgtgtatgtttctgctgtgtctattcatgcacattgccacattgtaccctcctccatttcacattatgt-ttatttaaatgtgtattacagGACTGAAAGTGCTTTGAAGTTTGGGTGGTTTTTCTTGTTTTACCTT

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 8
---------gttgtgaatatact-------tgtgtttttgttatttctgcacactatttcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
          |  |||  | | |       | ||  |   |  ||||  |    |||||   ||||   ||||  | |  ||| | | |  | | | || ||||| ||| ||||||||||| |||||||||||||||||||||||  ||
attgaagcattcatgagaacaataggcaaatatgcatgcatattttcatctttttattttgccttactgttgatcttgaatat-gctgc--tctttttttcagGAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCCTGTTTTATCTG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 7
-------gttgtgaatatacttgtgtt-tttgttatttctgcacacta--------tttcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
       ||  | |||  |  | |  | ||| || || |||  ||  |        |||  |||||   ||||  | |  ||| | |    | | | |||||||| ||| ||||||||||| ||||||||||||||| |||||||  ||
acctctggtactcaattaatatataatatttatttttgctgagcaaaaaaaaaaaatttggtcttactgttgatcttgaatat-gctgt--tcttttttgcagGAATGAAAGTGCTTTGAAATTTGGATGGTTTTTCATGTTTTATCTG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 9
-----------gttgtgaatatacttgtgtttttgttatttctgcacacta-tttcttcttatatttgacatagtgtattgttacaatgta--tgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
               | ||   |  |||| ||   |  |||   ||  ||| |||  |   |   ||||  | |  | ||||| || |||   | |||||||||||| ||||||||||| ||||||||||||||| |||||||| ||
ttcaatcctgcacaatcaaacaaagtgtgcttgcatattttgatcattctaatttggttacacccttgattttgaat-ttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
-----------gttgtgaatatacttgtgtttttgttatttctgcacacta-tttcttcttatatttgacatagtgtattgttacaatgt-atgtt-gcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
           |   | ||   |  |||| ||   |  |||   ||   || |||  |   |   ||||  | |  | ||||| || ||| || || | |||||||| ||||||||||| ||||||||||||||| |||||||| ||
ttcaatcctgcgcaatcaaacaaaatgtgcttgcatattttgatcattgtaatttggttacactcttgattttgaat-ttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------------------------gttgtgaatatacttgtgtttttgttatttctgca--cactatttcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
                                                                         |     |  | |   || ||   | ||     | |   |  | |      | |  |||| || |||| ||| |    | | ||| |||||||||| |||||| |||||||||| ||||||||| |    ||  ||
gtattcatgccacttaagatttttcctttaaaatatcttatctgctactgcgtcgtgtgttcctttatttagagggaaaacaaaaagagtattccagatagcatcgtagttaagagtcaaaactttcattgagat-gtgtgttgatttggt-tgtgt-gcagGACTGATAGTGCTCTGAAGTTTGGGTGGTTTTTCTTCACGTATCTG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 8
----------gttgtgaatatacttgtgtttttgttatttctgcacactatttcttcttata----tttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
            ||||  | | | ||| | ||||| || | ||   |   |||   || | |    | ||  ||    |     |||||  | | || ||||| ||| ||||||||||||||||||||||||||| ||||||| |||
ccaccatccatatgtgtgtgtgcatgtatgtttgt-atgtgtgtttatggttttacctgacaattttctgttatctgatcacactacaacatttcttacagGAATGAAAGTGCTTTGAAGTTTGGATGGTTTTTCATGTTTTATTTG

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|25803449|gb|CA759418.1|CA759418
EST:     ATCGCCCCCTTTACAATGCGATGAG                         GACTGAGAGTGCTTTGAAGTTNGGATGGTTTTTCCTGTTTTGCTTG
genomic: ATCGCCCCCTTTACAATGCGATGAGgttgtgaata ... tatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
EST: gi|11370676|gb|AU164981.1|AU164981
EST:     GTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG                         GACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
genomic: GTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAGgttgtgaata ... tatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
EST: gi|86889655|gb|CI299853.1|CI299853
EST:     ATCGCCCCCTTTACAATGCGATGAG                         GACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
genomic: ATCGCCCCCTTTACAATGCGATGAGgttgtgaata ... tatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
EST: gi|3760903|gb|C98157.1|C98157
EST:     GTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAG                         GACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
genomic: GTACCTGGAGCCTATGTGTTATGGTATCGCCCCCTTTACAATGCGATGAGgttgtgaata ... tatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
EST: gi|33683758|gb|CF311997.1|CF311997
EST:     ACAATGCGATGAG                         GACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
genomic: ACAATGCGATGAGgttgtgaata ... tatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacactatttcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG
                   atttgac  putative branch site (score: 4)
      tatttcttcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgaatatacttgtgtttttgttatttctgcacactatttcttcttatatttgacatagtgtattgttacaatgtatgttgcagGACTGAGAGTGCTTTGAAGTTTGGATGGTTTTTCCTGTTTTACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG