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

...acactctcagtctgatgatctagaattatttacttttatttacaccgttgtttttaggctgtttaacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g16190.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 2
acactctcagtctgatgatctagaattatt---tacttttatttacaccgttgtttttaggctgtttaacgtgattttgtggccacttgtgttatcttt-acagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
|||  |||| |   ||  | ||| |||| |   || || | || || | ||||| ||  |   |   ||    | | ||| |  | || | |   |||| |||| ||||||||||| || |||||||||||||| |||||||| || || || ||||| ||||| ||||||||||| |||||||||
acagactcacttgcatc-tgtagtattaatgaataattgttttaactctgttgtattctgtagg---aaaacaagtatgttgagatttttttccccttttacagGCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G033626_T01 (Zea mays), 3'ss of exon 2
----acactctcagtctgatgatc-tagaattatttacttttatttacaccgttgtttttaggctgttt-aacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
      |  | ||  ||     || ||| |||| | | | || |||  ||  |   || ||  ||||   ||    | | ||||     ||        ||| ||| ||||||||||| || || ||||||||||| |||||||| || ||||| ||||| ||||| || |||||||| |||||||||
tgtggaaaaccca--ctagcattcatagtattaatcaatattgttttaac--tcagttatattctgtaggaaaacaaatatgtgat--atttccccccttttgcagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G033626_T04 (Zea mays), 3'ss of exon 2
----acactctcagtctgatgatc-tagaattatttacttttatttacaccgttgtttttaggctgttt-aacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG------------------
      |  | ||  ||     || ||| |||| | | | || |||  ||  |   || ||  ||||   ||    | | ||||     ||        ||| ||| ||||||||||| || || ||||||||||| |||||||| || ||||| ||||| ||||| || |||||||| |||||||||                  
tgtggaaaaccca--ctagcattcatagtattaatcaatattgttttaac--tcagttatattctgtaggaaaacaaatatgtgat--atttccccccttttgcagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAGGTCTATGCAAATCCACTT

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP09161 (Chlamydomonas reinhardtii), 3'ss of exon 3
acactctcagtctgatgatctagaattatttacttttatttacaccgtt---gtttttaggctgtttaacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
    | |    | |     | ||   |  |  |  | |    ||| | |   ||   | | |   | | ||||         ||    |  |   |   |||| || || ||||||||||||||||| ||||| || || || || || || ||||| ||||| || ||||||||||| ||||||
---tttttgcacgggccgccaagttgtggtgcccctcaaagccactgctaaggtggctggccccctcaccgtgtcccctcacccttgggactccgccgcacagCCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 2
acactctcagtctgatgatctagaattatttacttttatttacaccgttgtttttaggctgtttaacgtgattttgtggccacttgtgttatc--tttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
  |||   | |    | ||    ||  | | |   | || |  ||   | | | ||   |  |  |  | |  |||  |||  |  ||||     | | ||||||||| ||||||||||||||||| || || ||||| || ||||| || ||| | || || || |||||||| |||||||||
ctacttatatttgattcatgcgtaa--actgaacgtgatgtgtacgaatatgtctaaaatactagaaatcaccttgatgcctgtgttgtttgtgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 3'ss of exon 3
--acactctcagtctgatgatctagaattatttacttttatttacaccgttgtttttaggctgtttaacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
    | | |  |  ||    |   |||| | || ||   ||||| ||  |   |  ||    | ||   |||    | |       | |||   |||| ||| ||||||||||| |||||||||||||| || ||||| || ||||| || ||| | || ||||| ||||| || ||||| |||
gttgaatgtgtgagtgtcagttgtgaataaatt-ctcagattta-actatgaatcatatctagattccggtgtgcatttaaattgctttgtgcacttttcagGCCAGAAATGGTTGTGGGCTGGTATCATTCACATCCAGGTTTTGGTTGCTGGTTATCTGGTGTGGATATAAATACTCAACAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16494 (Selaginella moellendorffii), 3'ss of exon 2
acactctcagtctgatgatctagaattatttacttttatttacaccgttgtttttaggctgtttaacgtgattttgtggc-cacttgtgttatcttt-acagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
                                              ||| || | |   | ||        || || |   ||  ||||   | |||  |||| | |||||||| || || |||||||| || ||||||||||| || || |||||||| || ||||||||||| ||||| |||
----------------------------------------------gttcttatcacatttttcttttctcttgtgggattcaagtgtgaagttttttgcagATCGGAAATGGTTGTAGGATGGTATCATTCACATCCTGGATTCGGGTGCTGGCTTTCTGGAGTTGATATCAATACTCAACAG

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|55908865|gb|AU032022.2|AU032022
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|38480043|gb|CF964132.1|CF964132
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58678825|gb|CK067512.1|CK067512
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|38476931|gb|CF961064.1|CF961064
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGNATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|38478871|gb|CF963004.1|CF963004
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58691729|gb|CK080416.1|CK080416
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58598852|gb|CK009380.1|CK009380
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|88290588|gb|CI666961.1|CI666961
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|568176|gb|D39011.1|D39011
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGTTGGTATCACTCC-ATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58679699|gb|CK068386.1|CK068386
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|6552265|gb|AU082093.1|AU082093
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTTGGATGTT
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTT-GGATGTT
EST: gi|86872923|gb|CI326920.1|CI326920
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58675840|gb|CK064527.1|CK064527
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58682525|gb|CK071212.1|CK071212
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58659705|gb|CK048385.1|CK048385
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|66926046|gb|CX112894.1|CX112894
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58677541|gb|CK066228.1|CK066228
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58680532|gb|CK069219.1|CK069219
EST:     GACCACGTCTTCCAGAGCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTG
EST: gi|218502937|gb|FG945477.1|FG945477
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|27548512|gb|CA767507.2|CA767507
EST:     GACCACGTTTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58597372|gb|CK007900.1|CK007900
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58677827|gb|CK066514.1|CK066514
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|572299|gb|D41810.1|D41810
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
EST: gi|58675425|gb|CK064112.1|CK064112
EST:     GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG
genomic: GACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTG

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: 73 (upstream exon), 74 (downstream exon)
Score: 37

ACGTCTTCGCCATGCCGCAGAGCGGGACGGGCGTCAGCGTCGAGGCCGTCGACCACGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaatcccct ... atctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgtttttaggctgtttaacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG
               gtttaac  putative branch site (score: 37)
                                           ttatcttt  putative PPT
                                           ttatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acactctcagtctgatgatctagaattatttacttttatttacaccgttgtttttaggctgtttaacgtgattttgtggccacttgtgttatctttacagACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG

- - - - - -ctgatga
- - - - - - - - - - - - - - - - - - - - tacaccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt