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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG

Basic information

species Oryza sativa
transcript LOC_Os12g34860.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                     | |     |   |  | |||  |||| |||  ||  |   |   | ||| || |    | |    |  |  | | |||||||   |  |  |  |||||||||||||||||||||||| |||||||| |||| ||||| || ||||||||||| |||||||| |||||||||| |||||| |||||  ||||||||||||| |
-------------------------------------------------------------------------------------tggcttcttccctgatatttgcttcaaatt--cgtgcctttacggaaacggtatgtagt-agttttgggcctctggctgacctatatatgttctttgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAACGACACATATTATGTTGATGGTCAAACAGTCTTAAGGTGTCATACCAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtg-tactttgaaccatatgattattg-ctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                        ||  || || | | | || ||||||||  || ||| |||  |  ||| || ||  | | |   | || |   || ||||||   |  |  |  | |||||||||||||||||||||| |||||||| |||| ||||| || |||||||||||||||||||| |||||||||| |||||| |||||  ||||||||||||| |
---------------------------------------------------------------------------------------atgtgct-gtgtgtttgttcttcagatt--cgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgt-gtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                              |   |||    |  |||  ||  |      || |  ||| || |    |||   | || |||| |||  ||               | |   ||||| ||||||||||| || ||||||||||||||||| ||  | |||   |||||||| |||||||| ||  | |||||||| ||| | |||||||| || |
---------------------------------------------------------------------------------------------gtacgttttcagtactcaagtttgcatctttctagaagtatcacttggtttt---caatgtgatcattattggtttt----------tggtaccagAACTTTGATGATGTGCTAGTCCCTGCTGATCATGTAAGCAGAAGTCTTAATGACACGTACTATGTAGACTCACAAACTGTTTTGAGATGTCATACGAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                             ||     ||   |||| ||       |||  |||   |||       |||    ||   | || |   |    |||||  |||  |   ||  |    || |||  |||||||||||||||||||  |||| ||| |||||||  | ||| ||||||||||||| ||||||||  ||||| |||||||||||||| ||||||| ||||| |
-----------------------------------------------------------------------------atcctatttatagcacatgagaga--tttggtcaatgtctg------cttccaaaattct-tattcatatttctatga--attcttatgccagaaaatatacttcttgcagAATTTTGATGATGTTTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGATCCTCAAACTGTCTTGAGGTGTCACACCAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgatt----attgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                           |  |  |||        |  || | | |  ||   | ||   |     | | | | ||||||   |    |||  |   ||  |  |  | |||  |||||||||||||||||||| |||| ||| |||||||  | ||| ||||||||||||| ||||||||  ||||  |||||||||||||| |||| || || || |
-------------------------------------------------------------------------------------------atcttatttataaggcatgggagttttggtcaatgtctgcttcca-aaattcttatccatatttctgtgaattcttatgccagaaattttacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgacccca-aggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                         |  | | ||| |      |  |  ||    ||     ||  |   ||  |  | |  |   |   || | | || |  ||| |     | |||  |||||||||||||||||||| |||| ||| ||||||| || ||| | ||||||||||| ||||||||  ||||  | |||||||||||| |||| || || || |
-----------------------------------------------------------------------------------------gatcctatttataaggcatggaagtttggtcaatgtctgcttccaagattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACGTCAGTAGAAGTTACAATGATACATACTACATTGACTCCCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 1
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                        |  | |  |   |||  | || ||| | |   ||          |||  ||   | |||||    ||               || ||       ||||| |  |  || ||  || ||| | |||  |||||||||||||||||||| |||| ||| |||||||  | ||| ||||||||||||| ||||||||  ||||  |||||||||||||| |||| || || || |
-------------------------------------------------------atcctatttataaggcatgggagttttggtcaatg----------tctgcttccaaaattcttatcca---------------tatttc------tatgaattcttatg-ccagaaagtc-tacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGGG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0011g01390.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgct-gcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGT--CATACCAGCG-
                                                                                    ||| |  | |  | |||   |||      ||  |  |    ||   ||    || |||||        | ||   |||       | | |      | || |||||||||| |||||||| |||| |||||||||||||||||   ||||| | ||  ||   | |  |     |    | |||| ||  | ||   |||||    | 
-----------------------------------------------------------------------------------ttttctttattgatgtttgacttt-----gtttgcatattgattagatagttttgaacttttgtaagagttatccatgc-atttttatgattgaatctacttgcagAATTTTTATGATGTCTTGGTTCCTGCTGATCATGTGAGCATGAGTTGCCATTGCA---AGTGGGCATCAGACAGAGCTGTTTTAGGATGGGGCATACTCATGA

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 3
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                        |  | |  |   |||  | || ||| | ||| ||          |||  ||   | |||||    ||               || ||       ||||| |  |  || ||  || ||| | |||  |||||||||||||||||||| |||| |||  |||||| || ||| ||||||||||||| ||||||||  | ||  |||||||||||||| |||| || || |  |
-------------------------------------------------------atcctatttataaggcatgggagttttggtttatg----------tctgcttccaaaattcttatcca---------------tatttc------tatgaattcttatg-ccagaaagtc-tacttcttgcagAATTTTGATGATGTCTTGGTTCCTCTTGATCACGTCAGTAGGAGTTACAATGATACATACTACATCGACTCTCAAACTGTCTTGAGGTGCCACACTACTG

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: 69 (upstream exon), 44 (downstream exon)
Score: 15

AGGGATTCTGAAGAACACTATTTACGACTACTTTGACAAGAATTTCTCTGGGAACTTTAACAAGTTCGATGACCTCTGCCCTCTTGTTTCTATCAAGCAGgtatgagtta ... cttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                          tgctgac  putative branch site (score: 15)
                atatgattatt  TA-rich tract