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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

Basic information

species Oryza sativa
transcript LOC_Os05g32110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   |||  ||    |||    |  | ||  ||          ||| |  | || | || ||    |      | ||||||||| | | |   | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||||||||||||||
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtc-tagattttatagcagaga--gggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   |||  ||    |||    |  | ||  ||          ||| |  | || | || ||    |      | ||||||||| | | |   | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||                              
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtc-tagattttatagcagaga--gggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgt---ttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
 |  || |  |      |   ||  ||||||    | |  ||  |   |    |  |||||       ||    ||||||||| | ||    | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattc--tttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgt---ttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
 |  || |  |      |   ||  ||||||    | |  ||  |   |    |  |||||      |||    |||||| || | ||    | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||||||||||||||
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgtctatattttatagcattgagagttcttatcagacattc--tttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttg--tcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  ||||  || || | ||| |   |   | ||  |    |  |  ||| |  ||| | |||     |  ||||   |||||||    |   || | || |||||||||||||||||||| |||||||| || ||||||||||||||||  || ||    |||||||| || |||||||| || |||||  | ||| ||||   
-ccatacgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgac-cttaacattgctctgatttatt-gcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATAACAATACAGTTGTACC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttg--tcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  ||||  || || | ||| |   |   | ||  |    |  |  ||| |  ||| | |||     |  ||||   |||||||    |   || | || |||||||||||||||||||| |||||||| || ||||||||||||||||  || ||    |||||||| || |||||||| || ||| |  | ||| ||||   
-ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgac-cttaacattgctctgatttatt-gcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA----------------------------------------------
                                        |  ||  || ||   ||  |||   ||| |   |||||     ||| |   | || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| ||  | ||| |||  | ||||||||| || |||||  | ||||| || ||                                              
---------------------------------------ttattagtatgaaacccaagttttggtttag---cttaatctgcatata--tttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
--atc--atagtggctccatatagaagttaaattt-gtcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  |||  | |  ||  | |  ||  ||||    |  ||    |  |  ||| |  ||  | |||     |  ||||   | |  |     |   || | |  ||||||||||||||||| || |||||||| || ||||||||||||||||  || ||    ||||| || || || ||||| || ||||| || ||  ||||   
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgc-----tctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
-atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttct-taacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  | | | |     ||  |  |  ||| | |||  |  |     || || ||| ||| |     |||  | | ||  |||||  | |    | | || |||||||||||||||||||| ||||||||||| |||||||| ||||| || ||||| || || ||||| || || ||||| || |||||||| ||  ||||   
gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattc-tggcaatttactatatccataacatcactcttgtttatt-gcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
atcatagtggctccatatagaagttaaatttgtcaaaatctt--ataccataaagttcatttttgttttttgttt--cttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   ||    |||  ||| |    | | ||   | |  |   |  | |||||    |   ||||    ||| ||||  |||||     ||| |   | || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| ||  | |||||||| ||||||||||| || |||||  | ||| | || ||
--tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatata--tttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaat-ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    | | | |     ||  |  || ||| | |||  |    | | || |    || | ||| | |   | ||||   |    || || |  |  | ||||||||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| || || ||||| || |||||||| ||  ||||   
gtgcttaaatttaaaacaactgaaaattacagttggta----cctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
----atcatagtggctccatatagaagttaaatttgtcaaaatcttataccata---aagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
     | |    |       |    |   |||    |   | | ||     | |   ||  | | |||||  |||| ||| |   |    |             ||||||| |||||||| || ||||||||||| || ||  | |||||||| || ||  | |||||||||||||| ||||| ||||||||  | ||||| ||   
gtaagttactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtga-------------cagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttg---cagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
     ||||  ||   |  | | ||    |  ||   |  | | |   | |  |  |||     |   |||       | ||| | |  ||| | ||   |||||||||||||||| || ||||| || || ||||| ||  ||||||| || ||  | |||||||| || |||||||| || || ||||||||||||||   
-agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagct--attacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC

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|58608092|gb|CK036125.1|CK036125
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTG
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTG
EST: gi|66918925|gb|CX105773.1|CX105773
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|58686271|gb|CK074958.1|CK074958
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAGCCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|29657169|gb|CB653444.1|CB653444
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|58654342|gb|CK043022.1|CK043022
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|33676440|gb|CF304679.1|CF304679
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|58660640|gb|CK049320.1|CK049320
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|29684532|gb|CB680807.1|CB680807
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC

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), 71 (downstream exon)
Score: 100

CTTAAGGCCCCAGGTCCTGGGTACACGTGCGGGCGTGCTATGATTGTCAGGCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
                           tcttaac  putative branch site (score: 100)
                                            tctgttt  putative PPT
        ttcatttttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

- - - - -gctccat
- - - - - - - - - - - - - - - - -caaaatc
- - - - - - - - - - - - - - - - - - - - - - accataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata