Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttttgttgatgaacatgaaatgcagcattaagtaactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA

Basic information

species Oryza sativa
transcript LOC_Os02g21250.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
-tgcttttgttgatgaa-catgaaatgcagcattaagt--aactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA
 || ||  | | |  ||  ||||||  | | | |   |  |   ||| | | || || |     |   | ||||   |  | | ||   || |  ||| |||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||||||| || || || ||||| ||||||||| | | |||||| ||||
ttgtttccgataaaaaaatatgaaa-acggtaatggttttagtgtttaccgaccgtttcc--gaccgttttaatccctattcagtgat-atgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA

upper sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
--------------tgcttttgttgatgaacatgaaatgcagcattaagtaactttttctgtcctttgcacaagctcatg----taatgattcatgattgtc--cattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA
               | |||||||   ||  |  ||||     |    ||||   |||  ||  ||  |    | |   |    |  | || | |  |       || |  ||| |||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||||||| || || || ||||| ||||||                   
gaagttaccgttttcgattttgtttccgataaaaaaatatgaaaacg-gtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------

upper sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 1
tgcttttgttgatgaacatgaaatgcag-cattaagtaactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA---
| ||||   |  |    ||    |   | |||  | | |   | |   |  ||| |      |||  | | ||||     ||||    |||  ||  | |||   ||||||| ||| | || |||||| | |||||||||||||||||||| ||||| || || ||||| | ||| ||||||||| | |  |||||  |||   
ttctttcaatcttttttattttgtttggacatgcattcatcatgttaattgttttcttctaatcaattca-gattttgttttgttttgttttcttttatagG---CTTGCCCCTCTATAAAAAACATTCTTCTTCTGGATTCTGAAGGGAAGCGTGTGGCAGTCAAATATTACTCCGATGATTGGCCAACAAATGCTGCAAAAT

upper sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
-----tgcttttgttgatgaacatgaaatgcagcattaagtaactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA
        |    || || |   |   ||| || | |     || |||  | | | |        ||  | | || ||| |||  |     ||||  || || |||| || ||||||||||| || |||||| | || |||||||||||||| |||||||| || || || ||||  |  || || ||| | |  |||    | |
aaacaaattcaaatttatcat--tcctatgtagtagttgagcacatttagttttcatgaactcgcctagtctgat-atttatg--taattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA

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|24208139|gb|AU225166.1|AU225166
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88302037|gb|CI667883.1|CI667883
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88355724|gb|CI629008.1|CI629008
EST:     GAAGGAAGGCACCGGGGCATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GAAGGAAGGCACCGGGG-ATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88355715|gb|CI628999.1|CI628999
EST:     GGAAGGAAGGCACCGGGGATCTACAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTCTTGCTTCTGGATTCTGAAGGGAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATT-TTGCTTCTGGATTCTGAAGGGAA
EST: gi|88724896|gb|CI748155.1|CI748155
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|163926048|gb|EG712328.1|EG712328
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88576575|gb|CI670720.1|CI670720
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88353711|gb|CI633102.1|CI633102
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAACAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88571060|gb|CI662433.1|CI662433
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|218496929|gb|FG959091.1|FG959091
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88719291|gb|CI742801.1|CI742801
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|163928617|gb|EG711178.1|EG711178
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88414612|gb|CI698719.1|CI698719
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88346751|gb|CI657302.1|CI657302
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88345106|gb|CI628360.1|CI628360
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88572505|gb|CI664076.1|CI664076
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|88325937|gb|CI649788.1|CI649788
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|117248583|gb|CT862782.1|CT862782
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
EST: gi|87012336|gb|CI293386.1|CI293386
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTC
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTC
EST: gi|88327839|gb|CI648236.1|CI648236
EST:     GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA
genomic: GGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAA

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: 37

CCAAACAAGTGGTTGATCTTACTGCTTTCGGTGGCCGTGTCTCCTCCACAGGAAGGAAGGCACCGGGGATCTAGAGGAGGCCATGGGAGAATTCTCCAAGgtaagtggat ... cgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA
                                     tccattttc  CT-rich tract
                     taatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttttgttgatgaacatgaaatgcagcattaagtaactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA

tgctttt
- - - -gttgatg
- - - - - - - - catgaaa
- - - - - - - - - - - -tgcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgt