Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttccacagcaaatttacttcatcttatcatctagattgttggaatagctgaatagagctcgacattccatcatacacatgggcataatttcgaagcaaatgctaactgtgcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA

Basic information

species Oryza sativa
transcript LOC_Os01g70170.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G828312_T02 (Zea mays), 3'ss of exon 2
gtgagtttccacagcaaatttacttcatcttatcatctagattgttggaatagctgaatagagctcgacattccatcatacacatgggcataatttcgaagcaaatgctaactgtgcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA
                          ||  |  ||    || |  |     |  ||||  | ||      |   |||||   |      |||| | || ||    || | | || ||  ||||||||    || ||||||||||||||| |||  |||||||| ||||||||||| || ||||||||| | || || || || || || || |||||||||||||
------------------------gtatgcttccacgacgagttct---ccacttgaactg-gcgttgtttcttatcat---cgcaaagataactccggag----tgatga-tgcgc-ttttcagGTCAACACGATGCCCGACCAAGCTTTGCACGCATTCATAGACCACGGCACTGTCTCGAGGACAGTTGATGCGAATGTGTCCGAGGCGGAAGGTGTATACA

upper sequence: LOC_Os01g70170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G134256_T02 (Zea mays), 3'ss of exon 4
gtgagtttccacagcaaatttacttcatcttatcatctagattgttggaatagctgaatagagctcgacattccatcatacacatgggcataatttcgaagcaaatgctaactgtgcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA
                          || || |||    || | |      |  ||||  | ||      |   ||||| ||||     |||| |  |          ||   |||| |||||||||    || ||||||||||||||| |||  |||||||| ||||||||||| ||||| |||||| | || || ||||| || || || |||||||||||||
------------------------gtatgttgtcacgacgagtttc---ccacttgaactg-gcattgtttcttatcat-cacaaaaaaataactctg----------tagtggtgcactttcagGTCAACACGATGCCCGACCAAGCTTTGCAAGCATTCATAGACCACGGCACCGTTTCAAGGACAGTTGATGCGAACGTGTCTGAGGCGGAAGGTGTATACA

upper sequence: LOC_Os01g70170.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtttccaca----gcaaatttacttcatcttatcatctagattgttgg-aatagctgaatagagct---cgacattccatcataca----catgggcataatttcgaagcaaatgctaactgtgcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA
|||||  | |  |    ||||  | | ||    ||  ||     |||||||  |  | |  || | || |      ||||   | | |||    |||    |   |    ||   | ||| |||| | |  ||||||||||| |||||||||||||||||||| |  |||||  | ||||| ||    ||||| |||||||| ||  | || || || || ||||||||  | ||||
gtgagccttcttatattgcaacctcagttggatttggcagt--aattgttgtcagcatcctaagaaagttatctaccatttacttaaacagttccataaataaggtccataatttactgccaact-tcctttttcagGTTTCAACCATGCCCGACCAAGCTCTCCAAGCATTTGTTGACCATGGTGTTGTTTCAAGGACAATTGATTCCAATGTATCTGAAGCTGAAGGCATTTACA

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|86435044|gb|CI106277.1|CI106277
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|86258478|gb|CI064831.1|CI064831
EST:     GACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: GACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|88228697|gb|CI228177.1|CI228177
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|86258385|gb|CI064738.1|CI064738
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|55410600|gb|CV722976.1|CV722976
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|88226047|gb|CI225963.1|CI225963
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|88249166|gb|CI249015.1|CI249015
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|86429112|gb|CI075793.1|CI075793
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|86505662|gb|CI148295.1|CI148295
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|2796567|gb|AA749861.1|AA749861
EST:     TCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: TCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|88223848|gb|CI223697.1|CI223697
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|88226513|gb|CI226429.1|CI226429
EST:     TACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: TACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|86501227|gb|CI143860.1|CI143860
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|55410654|gb|CV723030.1|CV723030
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA
EST: gi|38473510|gb|CF957642.1|CF957642
EST:     CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACC                         GTTTCTACCATGCCCGACCAAGGTCTGCTGGCATTCATCGACCACGGCACA
genomic: CTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 50 (upstream exon), 55 (downstream exon)
Score: 10

AGGTGCCAAGAAGCAGAGGTTGTTGTGGGCATCTACCAGTGTGAAGAACCCTGCATACCCAGACACTCTTTACGTGGATCCTCTCATCGGACCTGACACCgtgagtttcc ... gcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatcatacacatgggcataatttcgaagcaaatgctaactgtgcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA
                                   tgctaac  putative branch site (score: 10)
                                              cgctttc  putative PPT
                   ataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttccacagcaaatttacttcatcttatcatctagattgttggaatagctgaatagagctcgacattccatcatacacatgggcataatttcgaagcaaatgctaactgtgcgctttcagGTTTCTACCATGCCCGACCAAGCTCTGCTGGCATTCATCGACCACGGCACAGTTTCGAGGACAATCGACGCAAACGTTTCGGATGCTGAAGGTGTATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG