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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatccgaacctctgcatttccatttccttatacaaactcaatacacacattcatcgctgatattggatacccggtcctcttggcagATAATATCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAG

Basic information

species Oryza sativa
transcript LOC_Os01g04660.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G09820.1 (Glycine max), 3'ss of exon 2
gtatgtatccgaacct--ctgcatttccatttccttatacaaactcaatacacacatt--catcgctgatattggatacccggtcctcttggcagATAATATCCATAGTT-TGCCCTGTAATTATCTTTCTATCCGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAG
||| || | |         |  | |      || || ||     |  |||   |||||  ||    |  | |    |||    |  |  |||       ||| ||   || |  ||| || | |||||| |    || |||||    |||||||||||||||||||||||||| ||     || 
gtaagtttactggttcagttatagtatgtgatctttttattccttggataattacattaacaagattcttgtcatttactattttgttatggttagATTTATGCAGGTTTATTGCCTATAGTGATCTTTGTTGTTGTCTATATTCAAAGGAGAGATGTCTATGATCTTCATCATGCTGTGCTAT

upper sequence: LOC_Os01g04660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0006g02480.t01 (Vitis vinifera), 3'ss of exon 1
-------gtatgtatccgaacctctgcatttccatttccttatacaaactcaatacacacattcatcgctgatattggatacccggtcctcttggcagATAATATCCA-TAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAG
          |||   | |  ||    | |  | |     | || |      |||     |||| |   ||||   || |      |     |      |  ||| || |  | |  ||| |||  || |||||   | | ||| |   ||||||||||||||||||||||||||| || |   |||
gtaggtttcttgttatcaagtctaaatactatcctagttgtgtatatctctcatatgaggattc-tgattgatgagggttttttcatttgtgttatcagTTGTATTCAGTTCTGTTGCCTATAACCATTTTTCTCATCATCTATTTTCGTAGGAGAGATGTCTATGATCTTCATCATGCCATCCTAG
















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|33688362|gb|CF316601.1|CF316601
EST:     TGTTAGTTACCCGGTGAAACAAAGCACTGTNACCAGCATGGGGTGTTCCT                         ATAATATCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCT
genomic: TGTTAGTTACCCGGTGAAACAAAGCACTGT-ACCAGCATGGGGTGTTCCTgtatgtatcc ... ctcttggcagATAATATCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCT
EST: gi|218497722|gb|FG949370.1|FG949370
EST:     ATGTTAGTTACCCGGTGAAACAAAGCACTGTACCAGCATGGGGTGTTCCT                         ATAATTTCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCT
genomic: ATGTTAGTTACCCGGTGAAACAAAGCACTGTACCAGCATGGGGTGTTCCTgtatgtatcc ... ctcttggcagATAATATCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaactcaatacacacattcatcgctgatattggatacccggtcctcttggcagATAATATCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAG
                       cgctgat  putative branch site (score: 4)
                                           tcctctt  putative PPT
                          tgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatccgaacctctgcatttccatttccttatacaaactcaatacacacattcatcgctgatattggatacccggtcctcttggcagATAATATCCATAGTTTGCCCTGTAATTATCTTTCTATCCGTTTATATCGCTAGGAGAGATGTCTATGATCTTCATCACGCAACATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG