Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA

Basic information

species Oryza sativa
transcript LOC_Os07g14270.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G358059_T01 (Zea mays), 3'ss of exon 2
gtaaatt--ggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
|||||||    || ||||  | |              | |   |||| ||  ||| ||  |  ||||||||||||||||| |||||||| ||||| ||||||||||| || |||||||| || ||||| || ||||||||||||||||| ||||||||||||||||||||||| ||
gtaaattccaaaacatcagaagattggtggtttcagtttatttatgagtt--actcaac-acgtttcttgttgcagGTATTCAAACCTCCGAGGATTACAGGTTCTATGCCATTTCAGCCGAATACCCTGAGTTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
gtaaattggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
       |  |  |||| ||   |||     |   | |     | || ||| | ||| |  |||| |||||||||||| |||||||| ||||||||||||||||| || |||||||| || ||||| |||||||||||||||||||| ||||||||||||||||||||||| ||
-------gttaattcaaaacg--tcagaagaatggtgatttcagtttattagttaat-acgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 2
--------------------------------------gtaaattggaagatca-atacacctcattcagacactaaca----gatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
                                       ||   | |  | |||  |  || |   |   | | | | |    |||   |||   |||||  ||  | |   ||||||||| ||||||  |||||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||| ||| || || ||  | || || ||||| ||
gtaaactaaattgctatgttgaatagtcgggtattatactattattgttgctcatgtttacttttgtttaaaattgatattaagatatgtttggttgaat-gttgatatctctgcagGTATTCAAACCAGTGAGGATTACAGATTCTATGCTATTTCAGCTGAGTACCCTGAATTCAGCAACAAGGGTAAGACACTAGTCTTTCAATTTTCTGTTAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 2
-----------------------------------gtaaattgg--aagatcaatac-acctcattcagacactaacagatgatttttactgaattatttttcttgt---tgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
                                    |   |||   | | | | |     || |    || | ||| | ||| || ||  ||  | | | ||  | |   ||||||||| ||||||  |||||| ||||| |||||||||||||||||  ||||||| |||||||||||||||||||| || || ||  | || || ||||| ||
gtaaactaaattgctatattgaacagtcttgtattatttcttgctcatgtttatttttggctaaaattgatattaagatatgtttgtttttggctgaatgttgatatctatgcagGTATTCAAACCAGTGAGGATTACAGATTCTACGCTATTTCAGCTCAGTACCCTGAATTCAGCAACAAGGATAAGACACTAGTCTTCCAATTTTCTGTCAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------gtaaattggaagatcaatacacctcattcagacactaacagatgattt-ttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
                   |  |||   |  |||| ||    |  ||     |      | | ||   ||  || | |     |  | | ||||||||||| |||  ||| |||||||| |||||||| |||||||| |||| ||| |||||||| |||||||| || ||| | ||  | || ||||| || ||
gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgtgctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaattggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
|||  ||  | || || |  |     || |  |||| |   ||  | |    | ||||||   |||  ||||||||||||||||    ||||||||||| ||||||||||| ||||| || | ||| || || |||||||||||||| ||| | ||  | || |||||||| ||
gtatgtttcatgaccagtg-atgatgttgattcactgattcatattctcatgtcaattataactctc-ttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA

upper sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------gtaaattggaagatcaatacacctcattcagacactaacagatg-atttttactgaatt--atttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
                                  |   | ||    ||         | |||  |||  | | |  || |  || | |  | |  | |  ||| | |  ||||||||||||   |||||||||||| ||||| ||||| ||||| |||||||| |||||||||||||| ||||| ||  | ||  | || ||  |||| ||
gtattattttcatacacattcttatacctatttggggcaatgtttcattctctttattaatttggactttgaaatgtgtaacttgatttgacttcaatggtctggatatagGTATCCAAACAAGTGAGGACTACAGATTCTATGCTATATCAGCTGAGTACCCTGAATTCAGCAACAAAGATAAGACATTAGTTTTCCAATTTACTGTTAA

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|58660986|gb|CK049666.1|CK049666
EST:     TGGAG-TCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|29675378|gb|CB671653.1|CB671653
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|6012783|gb|AU078600.1|AU078600
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTNAGGACAAAG                         GTATCCAAACCTCTNAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|29675242|gb|CB671517.1|CB671517
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|88688874|gb|CI732450.1|CI732450
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|88312709|gb|CI587617.1|CI587617
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGATGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|88311943|gb|CI577549.1|CI577549
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|88689333|gb|CI732909.1|CI732909
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|58604287|gb|CK014815.1|CK014815
EST:     TGAATGGAAGGGCACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|88688533|gb|CI732109.1|CI732109
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
EST: gi|88348476|gb|CI629965.1|CI629965
EST:     TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAG                         GTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC
genomic: TGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACC

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), 74 (downstream exon)
Score: 165

GAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGATGAGAACATGGCTGGTGAATGGAACCACACATCTGGGAAGTGGAATGGAGATCCTGAGGACAAAGgtaaattgga ... cttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA
             cactaac  putative branch site (score: 165)
                                     ttatttttcttgtt  putative PPT
                      atgatttttactgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG