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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

Basic information

species Oryza sativa
transcript LOC_Os01g71230.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 3
gtgagc---tgcttaatcactgtta--tgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
|| |||   ||  | |||  | | |  |  ||    |  || |    |  ||||  | || |       |  |  |||      |   |  ||       |||| |||||||| ||||| ||||||||||| |||||||| ||||  || || || ||| | || || || || || ||||| || ||  ||||||| ||| 
gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT

upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 3
-----------gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttt---tccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
            |||   |  |  | |   ||   ||| | ||| ||| |   |  |||| || || |       |  |  |||   ||||||       ||       |||| |||||||||||||| |||||||| || |||||||| ||||  || ||||| ||| | || || || || || ||||| || ||  ||||||| ||||
gttagtagcatttgacacgtctttttagcttttcaccactcttttttgcat-ttgtcagatttattttgctttggtaaaaattga--aactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
------gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
      ||   ||  |||||      |    | |  |||||| ||  | ||||  |   ||  |||    |   |||||   |  ||| |  || |  || ||||  |||| ||||| || || || ||||| |||||||| |||   |||||||| || || ||||| || |||||||||||||||||| ||||||| ||| 
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacac-agATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagctgcttaatcactgttatgccattg--tttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcac-taccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
       | ||   | || | |    |||   | |||  |  | | |  |  ||  ||| |  |        ||| |  | | |    || |  |  |||||  |||| || || || ||||| ||||| |||||||| |||   ||||| || || || ||||| |||||||| ||||| |||||| ||||||||||||
-------gtttgtgctct-tcagaaaattaaatctctcttgtgttaattgt-ttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC

upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
                                          ||| |  |  | |  |      | |  || |      ||       |   | |  ||   ||   |   ||    | || | |||  || |||||  |||| ||||| || |||||||||||||||||||||||||  ||||| || || ||||| || || ||||| ||||| || ||  ||||||| ||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgc--tatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
---------------------gtgagctgcttaatcactgttatg------ccattgtttcttgtaggctcacagaattgtta-tataccattgcattttgc------ttaacttttccctgcactac-cagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
                     ||    | |||  |   | | |||      | |||||  | | |    |  |||  || ||  |||   |     | |||       || ||| |    |  | ||  |||||||| || |||||||| || |||||||| |||||||||||||  |||||||| || || || || || ||||| ||||| |||||| |||| || || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagctgcttaatcact---gttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactac-cagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
 | | || |       ||    || ||| ||  |   |||     ||    ||| | | |  |||  ||  || |||||   |||    || | | | |||||||| || || |||||||| || ||||| |||||||||||   ||| |||||| |  ||||||| || ||||| |||||||||||| |||| |||||||
-ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

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|8956759|gb|BE230562.1|BE230562
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|58598732|gb|CK009260.1|CK009260
EST:     CATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: CATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|2798195|gb|AA751489.1|AA751489
EST:     CAAAAAGAGCAAGAAC                         ATTCTGTTCGTAATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: CAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|88974533|gb|CI022074.1|CI022074
EST:     TGAAGACCATCACTGGTGTGATCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|88847212|gb|CI011155.1|CI011155
EST:     CACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: CACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|88578321|gb|CI687244.1|CI687244
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|7378325|gb|AU088596.1|AU088596
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|86416314|gb|CI030325.1|CI030325
EST:     CCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: CCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|58690965|gb|CK079652.1|CK079652
EST:     AAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: AAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|58677856|gb|CK066543.1|CK066543
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|287091|gb|D15896.1|D15896
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|4716582|gb|AU057698.1|AU057698
EST:     GAAGACCATCACTGGGTGTGANCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: GAAGACCATCACT-GGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|88591468|gb|CI707505.1|CI707505
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|88467066|gb|CI696425.1|CI696425
EST:     TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: TGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|86412655|gb|CI067060.1|CI067060
EST:     GCCGTGTCACTATCAAAAAGAGCAAGAAC                         ATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
genomic: GCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGAC
EST: gi|16574056|gb|BI801352.1|BI801352
EST:     CCGTGTCACTTATC-ATAAGAGCAAGAAC                         ATTCTGTTCGGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGA
genomic: CCGTGTCAC-TATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTC-GTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGA

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: 74 (upstream exon), 75 (downstream exon)
Score: 201

GCAGAGTAGGAGCGAGAAAAAGAGCAGGAAAGCCATGCAGAAACTTGGCATGAAGACCATCACTGGTGTGAGCCGTGTCACTATCAAAAAGAGCAAGAACgtgagctgct ... gcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
                              gcttaac  putative branch site (score: 201)
                                    cttttccctgcact  CT-rich tract
      aattgttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT