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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgtgacagctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccag

Basic information

species Oryza sativa
transcript LOC_Os04g52900.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G084181_T01 (Zea mays), 5'ss of exon 22
GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgtgacagctgacttttttaaaa---aatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccag---
||||||||| || |||||||| ||| |||| ||||| |||||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||        | |    || |   | |||   ||  |  ||||  ||  | ||    |    |||   |    | | ||||||| || |   |  |      |    
GCTCTCAACTTTCGTTCTCATCGGCTTTGTCAGCACCATGTCTCTTTGGGCTATCATGCCACTCCTGATTTTGTTTTATGCAGCTTACCTCTATTACCAGgtatgacaaccaaaaactacatcgctgaaatcaaagttgcattatggaacgcatcaaaa----taagcacc---accatgacatc-cacatgggaatgactaaaaacc

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA06G46940.1 (Glycine max), 5'ss of exon 24
GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtac-ttttgtgacagctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccag-
 || || ||||||||||| || ||||  || ||||| || || ||||||||||| |||||||||||||| || |||||||||||||| || ||||||||||||       |  |   |   |  ||| | |    | |  | | ||||  |||   |  || |  |  ||  ||||     |  |||    |  | |    || 
ACTTTCGACATTTGTTCTTATAGGCACCGTGAGCACCATATCCCTGTGGGCTATAATGCCACTTCTGATCTTCTTTTATGCAGCTTATCTATATTACCAGgtatgccccatatcttgtccttagttttagagtcgtctcatta-gatt--attcacatgccaagttggttttatct-acttttgcattatggattctcttgaga

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 5'ss of exon 23
GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgta---------cttttgtgaca----gctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgac-atctcatacctgtcttttcccag---------------------
 || |||||  || |  | ||||||||||| |||||| |||| |||||||| |||||||| ||  || |  | || |||| |||||| || ||||||||||||         |||||   ||     |||  ||   || |  | || | ||  |    || |    |    | ||      |||   |||   | ||||| ||||  | ||  |                      
TCTTTCAACTGTTATCTTGATTGGCATTGTCAGCACTCTGTCCCTGTGGGCCATCATGCCCCTGTTGGTCGTGTTCTATGGAGCTTATCTGTATTACCAGgtaacctacatactttttaaacgcaatgctatctacattcatgactacagatcgagacatggaaaactgagaccaaaag---gaacactgattgtgtcatatctgttgtgtcataacctgatttttccttattgtag

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT2G34660.2 (Arabidopsis thaliana), 5'ss of exon 23
GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttt-tgtgacagctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccag
 || |||||  | ||  | ||||||||||| |||||| ||||  ||||||| |||||||| || ||| | || ||||||| |||||| || ||||| |||||| | |   |   | | |     |||||| ||   | |||||  |    |  |  |     |      ||| |  ||  | | ||||| | | |   | |  
TCTTTCAACTGTAGTGTTGATTGGCATTGTAAGCACTTTGTCCTTGTGGGCCATCATGCCCCTCCTGGTCTTGTTTTATGGAGCTTATCTTTATTATCAGgtaatgtaccttctaaccgcagcatttaaataactgagattaagtaacagaaagagaaaaggacacagatgattgatgtta-cacatacttttttagcctc--

upper sequence: LOC_Os04g52900.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 5'ss of exon 23
GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgtgacagctgacttttttaaaaaatatatattaaagattgtatt-gttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccag-
 || || || ||||| || |||| |||||| ||||| || || |||||||| || |||||||||||||| || ||||||||||| || || ||||||||||||  ||| | |||  | |  |  |     ||    || ||||| || | ||  || ||  |    | |  |    | ||   | | |||| | |  |  |   
CCTTTCCACTTTTGTACTGATTGCCATTGTCAGCACCATATCCCTGTGGGCCATAATGCCACTTCTGATATTGTTTTATGCAGCCTATCTATATTACCAGgtaggtttctcacatgtcatgtagtgtctcaac---tactaaagcttttcttcatttgttttctgatttgcagagataac-cataagacctatttgatatccat

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|66912933|gb|CX099781.1|CX099781
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58692501|gb|CK081188.1|CK081188
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58688905|gb|CK077592.1|CK077592
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58693623|gb|CK082310.1|CK082310
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58613211|gb|CK040923.1|CK040923
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|29621686|gb|CB626697.1|CB626697
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG
EST: gi|58612973|gb|CK040685.1|CK040685
EST:     CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAG                         ACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAANGTCTCCTGTG
genomic: CTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgt ... cttttcccagACTACGTCTCGTGAGGTAAAGCGCCTGGATTCCATTACAAGGTCTCCTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTCAACATTTGTTCTCATTGGCATTGTTAGCACTATGTCTCTGTGGGCTATCATGCCACTTCTGATTTTATTTTATGCAGCTTACCTCTATTACCAGgtacttttgtgacagctgacttttttaaaaaatatatattaaagattgtattgttagtcctaacttcttgaatcttgacatctcatacctgtcttttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT