Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttttggtgccctttccttgtgctgcgcttaatacttcagttcaatccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA

Basic information

species Oryza sativa
transcript LOC_Os07g15880.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
------------agttttggtgccctttccttgtgctgcgcttaatacttcagttcaatccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
             | |||| |  |  || |  |||    |   | |  || |||||  |    ||     | |  | |  | | |||| |        ||    || | ||||| || ||||| || |||||||| || ||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| |
taccttctcagttgatttgttatcacttacaagtgtc-tggccattgtttaagttctgt---tctggtgttgggagtaaaattgatatgt--------tggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 2
-----agttttggtgccctttccttgtgctgcgcttaatacttcagttcaatccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
         ||| | |  | |   |     | |  |   ||    |||  |      |||   | | ||    | ||| ||  || |      || |   | ||||| || ||||| || || |||||||||||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| |
ccttctaaattgattcgttattactaataagtgtgtgtgaccattgtttgagttctgttatggtggttgt---agtaaaattgatatgttggttaatg--tgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTA

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 3'ss of exon 2
agttttggtgccctttccttgtgctgcgcttaatacttcagttcaatccacct-taacatagctggatgactaatatatatttaaca--tgtactacc-tacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
     ||   |   ||  |  ||      ||  |  |   ||| |    |     |   |   |   | || | ||| ||  |   |    |  ||     ||||| ||||||||||| || ||| |||||||||| |||||||| |||||  |||| ||||| || |||||||| ||  | ||||| |||||||| || ||||
---cctgagactgattagtcatgaaat-tttgttgttctcgttgagcgtaaaaacagtcttcttaattcacaagtatgtagcttgtaaccttgttattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTCATCTATGACGTTCGTGCTCGACCTTACCTTGTTGAGAGTACATCCGGAA

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 3'ss of exon 3
agttt-tggtgccctttccttgtgctgcgcttaatacttcagttcaat--ccaccttaacatagctggatgactaatatatatttaacatgtactacc-tacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
|||       |    || |||   ||    || ||| |    | |||    || ||| |     |   || | || ||||| |||  | ||    |   |  |||| ||||||||||| |||||| |||||||||||||||| || ||||||||||| ||||| || |||||    ||  |||| || ||||| || ||||| |
agtaaacaaggttgatttcttagtctagttttgatagtcgtttacaaaagtcatcttgatgcgcc---attaatagtatatctttg-cttgcttgattatgtagGTCTACCCTGAGGGTACTCACCTTATGATTCCATGGTTCGAAAGGCCAATCATCTATGACGTTCGTGCAAAGCCTTATCTAGTTGAGAGCACATCTGGGA

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 3
---agttttggtgc-cctttccttgtgctgcgcttaatacttcagttcaatccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
     ||||  |||  |  |  || ||       |  |  | | |||   |     | | | || ||   |     ||  ||| ||  ||||   ||  | ||||| || ||||||||||||||| | ||||| ||||||||||| |||||| | || |||||||||||||| || ||  |||| |||||||||||||| || |
ttttcttttcctgcatcactaattctgtaatttctgtttttcctgttgtttgtcattcaccgtaactcattagaacat-catacttt-catgggata--tgcagGTTTATCCTGAGGGGACTCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGA

upper sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 3
agttttggtgccctttccttgtgctgc--gcttaatacttca-gttcaatccaccttaacata-gctgga--tgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
      |     |||| | ||     |    |   || || | |||    | |  ||  |||   ||| |  | | ||  | ||  |    |  |   |  | ||||| || || ||||| |||||| | ||||| ||||||||||| |||||| |||| |||||||||||| | || ||  ||||||||||||||||||| || |
------gagtttcttttcctgcatcactaattctgtaatttatgtttttcctattttgtcattcactgtaattcattagaacatcatacttagatgggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTCATCTATGATGTCCGTACGCGCCCTCATCTTGTGGAGAGTACTTCAGGGA

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|32948492|gb|BP185064.1|BP185064
EST:     GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAG                         GTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
genomic: GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
EST: gi|218496989|gb|FG950832.1|FG950832
EST:     GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAG                         GTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
genomic: GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
EST: gi|27578030|gb|CB000725.1|CB000725
EST:     GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAG                         GTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
genomic: GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
EST: gi|117233393|gb|CT848123.1|CT848123
EST:     GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAG                         GTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
genomic: GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
EST: gi|58686687|gb|CK075374.1|CK075374
EST:     GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAG                         GTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
genomic: GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
EST: gi|11118160|gb|AU163348.1|AU163348
EST:     GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAG                         GTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC
genomic: GTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATC

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: 75 (upstream exon), 75 (downstream exon)
Score: 57

CGGCGGCACGGCCGTGTACGCCGCCGTCAACAGCCTCTACAACGTCGAGGGTGGCCACCGCGCCATCGTCTTCAACCGCATCCAGGGAATCAAGGACAAGgtaaccggac ... ctacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA
                         taatatatatttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttttggtgccctttccttgtgctgcgcttaatacttcagttcaatccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - -tggtgcc
- - - - - - - - - - -tgctgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatgt