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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgctggccacgggaacctgcagaaacagattatcaactagtaattaatttgaatgcaaagtttgatccggaattgatgaaaacactgtgcatgaacctctctgtcag

Basic information

species Oryza sativa
transcript LOC_Os03g53150.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G077356_T01 (Zea mays), 5'ss of exon 2
GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTC---ACCGCAACTGgtaaatcgc-----------tggccacgggaacctgcagaa-acagattatcaactagtaattaatttgaatgcaaagtttgatccggaattgatgaaaacactgtgcatgaacctctctgtcag------------------------------
   || |||||||||||||||||||||||||||| ||||  |||||||||||||||||||  ||| ||  ||||||||||||||||||||   ||||||||||||||||| |           | | ||  |||| |||||| | |||   |    |   | | | |    ||  || | |  |  | |  | | |  |||  || || |  ||| |    |   |||                              
---GCGCCCTACCTGCGCAAGGTGGACCTGAAGACGTACGGCAGCTACAAGGACCTCTCCGCTGCACTCAAGAAGATGTTCGGCACCTTCGTCACCGCAACTGgtaaatctcaccccggcccgttggcataggaatctgcagcatacaagcttgtgaaccgaactgataccgatcgccacgcctt-tacaaattcggcgaatgcattgagt-tgagctgaacccacagaagctgtgcgtccatgatccgtcttaccag

upper sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G159285_T01 (Zea mays), 5'ss of exon 2
GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgc----------tggccacgggaacctgcagaa---acagattatcaactagta------------attaatttg---aatgcaaagtttgatccggaattgatgaaaacactgtgcatgaacctctctgtcag
|| || ||||||||||||||||||||||||||||||||||||||||||| ||| |||||| |||||||| ||||||||||| ||||||||||| || | |||||||| |          | | |   |||| |||||||    |||| ||   ||||   |            |  || |||   ||||| ||| |    || ||| | ||  || |    | ||||| ||    |  |||
GGCGCGCCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACACGGAGCTCTCCGTTGCTCTGAAGAAGATGTTCAGCACCTTCACCACATCCGgtaaatcacatttaccctgttggcgtaggaatctgcagagcatacagtttgcgaactgacaccagtcgtctttacaaacttggcaaatgcgaagctga--cctgaactcatagaagctgcatccatgatccatcttaccag

upper sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 3
---GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgctggccacgggaacctgcagaaacagattatcaactagtaattaatttgaatgcaaagtttgatc-cggaattgatgaaaacactgtgcatgaacctctctgtcag
   || ||||| |||||||||||||||||||| |  |||||||| |||||||| ||  | ||   |||  ||   || |||||| || ||||||||      ||| | |  |    ||    ||||| |  |   |   |||   |   |  ||||  |   ||   |     |    |  | |||    |  ||   ||||  ||           
GATGGAGCACCTTACCTGCGCAAGGTGGACCTCACAATGTACAAAAGCTACAAAGAGTTATCTGATGCCTTGGCCAAAATGTTCAGCTCCTTCACCATG---Ggttagttacca--ca-aaaaaccttcctacgtatcatattcccctctctttaaactacttgtttaccacaactatgtcactgaaaggataaccacgcatacac-----------

upper sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G14550.1 (Arabidopsis thaliana), 5'ss of exon 2
---GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgctggc-cacggg---aacctgcagaaaca-------gattatcaactagtaattaatttgaatg-caaagtttgatccgga----attgatgaaaacactgtgcatgaacctctctgtcag-----
   || || || || || || ||||| ||||| |||||||||| |||||||||||| |||||   |||  ||   || |||||| || |||| |||     |    | |  | | |  |   |   ||    ||  |  |       | |||   || | |  ||  ||| || |  | |||||  |||  |    | | || || |   |  |  |     | |   | |      
GATGGAGCTCCTTATCTTCGGAAGGTTGACCTCAAGATGTACACCAGCTACAAGGATCTCTCTGATGCCTTGGCCAAAATGTTCAGCTCCTTTACCATGGgtatgcattttcagacatataagtcgaattatcattattatttttgtgtttacttacaattttttctttttaacgatacagttttttccatatacgactaattaatatgataagttttgggattttgattaattaag

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|27547092|gb|CA765289.2|CA765289
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|87032502|gb|CI266142.1|CI266142
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|58603884|gb|CK014412.1|CK014412
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTAC
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTAC
EST: gi|88984831|gb|CI011778.1|CI011778
EST:     CTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACCATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: CTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|86595238|gb|CI262476.1|CI262476
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|8860135|gb|AU097453.1|AU097453
EST:     TTCACCGCAANCTG                         GGAACAATATGAATGAGGTGAATGNCTCTGATGCTGTTACAACTTATGAA
genomic: TTCACCGCAA-CTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATG-A
EST: gi|87013733|gb|CI269232.1|CI269232
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|58686964|gb|CK075651.1|CK075651
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|8856221|gb|AU093539.1|AU093539
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGNAATGGCTCTGATGCTGTTACAACTTATGAA
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTG-AATGGCTCTGATGCTGTTACAACTTATGAA
EST: gi|87013621|gb|CI269120.1|CI269120
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|87018381|gb|CI265673.1|CI265673
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|8856770|gb|AU094088.1|AU094088
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|58679632|gb|CK068319.1|CK068319
EST:     TTCACCGCAACTG                         GGAACCATATGAATGAGGTGAATGGCTCTGATGCTGTTACCACTTATGAAG
genomic: TTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|88203351|gb|CI203200.1|CI203200
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|18387131|gb|BM420329.1|BM420329
EST:     -GACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAAC-ATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|88456767|gb|CI544704.1|CI544704
EST:     ACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: ACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|86602330|gb|CI262799.1|CI262799
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|87018941|gb|CI256826.1|CI256826
EST:     GGACCTGTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|88242474|gb|CI242323.1|CI242323
EST:     AGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: AGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
EST: gi|58596036|gb|CK006564.1|CK006564
EST:     GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTG                         GGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG
genomic: GGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAG

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: 62 (upstream exon), 72 (downstream exon)
Score: 71

GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgct ... tctctgtcagGGAACAATATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAGACAAGGATGGTGACTGGATGCTTGTTGGAGATGTCCCGTGGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGCACCCTACCTGCGCAAGGTGGACCTGAAGATGTACAACAGCTACAAGGACCTCTCCCTTGCTCTGCAGAAGATGTTCGGCACCTTCACCGCAACTGgtaaatcgctggccacgggaacctgcagaaacagattatcaactagtaattaatttgaatgcaaagtttgatccggaattgatgaaaacactgtgcatgaacctctctgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG