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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA

Basic information

species Oryza sativa
transcript LOC_Os06g06880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G041822_T02 (Zea mays), 3'ss of exon 2
----tttctcagtga-atctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
     |    ||||  || |||| || ||      ||||   || |  ||| || | ||  || ||| |||| | |||  ||| |    | ||||    | |||||| || |||||||||||||| || || || || |||||||||||||| |||||||| ||||| ||||| ||||| |||||||||||||| || ||  |||
aaacatctagagtgctatatctgttg-agctgtgaattacaattttggttgtgc-actgctttcatt-accattgact--tttttaactgaatctaacttcacagGTCGTAGAGGATGGCTATGAGTTTTTCGCAAATCGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTTGACAATGCTGGTGCACTGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
----tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
     |    ||||    |||| || ||      | || | || |  ||| || |||| ||| ||| |||| | ||| || |      | |||| || | |||||| || |||||||| |||||||| || || || |||||||||||||| |||||||| ||||| ||||| ||||| ||||| |||||||| || ||  |||
aaacatctagagtgctcatctgttg-agctgtgaaatactattttggttgtgc-attgccttgatt-accattgacttctcttcaactgaatctact-tcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G64040.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------tttct-cagtgaatctctgctgta-gtgaactattat------tgttattattgagcgattgtcttt-atttaccactcactgctttgt----gctggg-atcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
                      | |||   ||   |||||  |||         || ||      |   | || ||  ||| |   | | ||||| | ||     | |  |    | ||    | ||  |    |||||||||| || || |||||||||||||| ||  | ||||| ||||| |||||||| || || ||||| || || |||||||| || || || || ||||
gtaatattttgctttagacatgtatctgtggtacgtctcttttgtttacttgtcatcataggacctacaaataatggacgaatacttatgatttatctcttttaacctcattgaagttgattgttttgccctttagGTTGTGGAAGACGGGTATGAATTCTTTGCAAATAGACAGCTAGTAACGATATTCTCGGCCCCAAACTACTGCGGAGAGTTTGATAACGCAGGAGCAATGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------tttctcagtgaatctctgctg------------tagtgaactattatt--gttattattg--agcgattgtc-tttatttaccactcactgctttgtgctgggat-cttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
                                                           ||||| |||| | |   |||            ||   ||  || | |  ||| ||| ||  ||    |||  ||| || ||||  |   | |||        || ||  ||   |||||||| || ||||| || || |||||||| ||| | || || || || ||||||||||||||||| || |||||||||||||||||||| || ||  |||
gtaaagctaaaatttattccttgagttctctcttttgatttctctggattggtttgttcttctctgtgactgttctctgaattcagagggttaagaaatcataactcagttgttaatgcaaggatctgtagttttttcaccaagccaagttttacttaactatactgttcctgcagGTTGTAGAAGATGGATACGAGTTCTTTGCAAAGAGACAACTAGTGACAATATTCTCTGCACCCAATTACTGTGGCGAGTTTGACAATGCTGGTGCATTGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
---tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
   |  ||  |||  | |   |||| || |  | | ||| || ||  |    || |    ||| ||   |||      ||||  || ||   |    |  ||||||||||| ||||| ||||| || ||||| ||| | ||||| || ||||||||||| ||||| || || ||||||||||| |||||||| || || ||||
acatccctgtgtgtttattatctgtggtta--tgtgattttttttggttga-gactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDO97337 (Chlamydomonas reinhardtii), 3'ss of exon 4
---------------------------------------------------------tttctcagtgaat--------ctctgctgtagtgaactattattgttat-tattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
                                                           | |||  | |         | |  ||   | |  ||  | | ||    |||    |    ||    |  | |     |||    |   || | || |  | |   |||| |||||||| || || || ||||| || |||||||||||||| ||||||||||| || || ||||| || |||||||| || |||||||| |||||||
gtgcgggtcgtcgcctaggtgttccgcgggtttatggggttggcggaacacgcatcgcatgtcaagggacggggggtacccgactccgggggtcttgtgtggtcccgtatctgcccgaagtgcagagctcctctgaactttgcttgtcttgcatgtggtattgtagGTGGTGGAGGAGGGGTACGAGTTCTTCGCAAAGCGCCAGCTTGTGACCATATTCTCGGCGCCGAACTACTGCGGCGAGTTCGAGAATGCGGGAGCGATGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
tttctcagtgaatctctgctgtagtgaactattattgtta-ttattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctg-acagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
 |   ||||     | |  ||  ||       | |  | |  |  ||   | | |  | | | |||      ||| | ||||| ||||| | |  || |||||||||||||||||| || || || || ||||||||||| || || || || ||||||||||| || |||||||| || ||||| |||||||| || ||||
-tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgc-gggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
-tttctcagtgaatctctgctgtagtgaactattattgtt-attattgagcgattgtcttta--tttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
 ||  | | |  |  | |   ||  ||       || ||  ||  || | |  |  | |  |  | |   | | | ||  ||| | |||||| | | |   ||||| || |||||||| ||||||||||| || ||||||||||| || || || ||||||||||| || || ||||| || ||||| |||||||| || ||||
attgattaatttacttttttcgt--tgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcg-tgggat-tccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
tttctcagtgaatctctgctgtagtgaac-tattattgttattattgagcgattgtctttatttaccact-cactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
        |||| ||| | ||   |  || | |   |   |  |     |  || | ||  ||    |||   ||| | |||| |||||| ||   | |||||| || |||||||| |||||||| || ||||||||||| || || ||||| || ||||| || || |||||||| || ||||| |||||||| || ||||
gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccatacttttatattctttgtatactatgctgatctgtg-tgggatgttacat-acagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

upper sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S22_185V6.1 (Physcomitrella patens), 3'ss of exon 3
---tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
   |||   | |    |  ||   |   |     | || | ||  |||     |||     | | |  ||   ||||   ||||    ||   || |   ||||| ||||||||||| ||||| || |||||||| |||||||| || || || ||||||||||| || || ||||| || ||||| |||||||| |||||||
gattttacaaattgtacaatgtgattcagtctcctaatgggtagaattaccttattcctggtgtgtttcaagtactgacatgtgt---gaatgtcacatgcagGTAGTGGAGGATGGTTATGAGTTTTTTGCTAAACGCCAGCTGGTCACTATTTTCTCTGCACCAAATTACTGTGGTGAATTTGATAATGCGGGTGCGATGA

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|88273209|gb|CI388665.1|CI388665
EST:     ATCTAGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: ATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|88277788|gb|CI398590.1|CI398590
EST:     ACACATGATGTAGATCTAATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: ACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|89164786|gb|CI101874.1|CI101874
EST:     CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|86260978|gb|CI066653.1|CI066653
EST:     CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|86498970|gb|CI141603.1|CI141603
EST:     CTAGATCTGATCTGCAGGGCTCACCAG                         GTTTTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: CTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|86425088|gb|CI070185.1|CI070185
EST:     CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|163917674|gb|EG712072.1|EG712072
EST:     CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|88384046|gb|CI548387.1|CI548387
EST:     CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: CTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
EST: gi|86501423|gb|CI144056.1|CI144056
EST:     AGATCTGATCTGCAGGGCTCACCAG                         GTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA
genomic: AGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATA

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: 64 (upstream exon), 44 (downstream exon)
Score: 8

GGGTGAGAATGACAGGGGTGTATCATACACTTTTGGAGCTGATAAGGTCGCTGAGTTTCTCCAGACACATGATCTAGATCTGATCTGCAGGGCTCACCAGgtatgttttg ... tctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA
                    cactcac  putative branch site (score: 8)
                                          tcttctct  putative PPT
     attgtctttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA

- - - -gtgaatc
- - - - - - - tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctgg