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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgttgcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgattatgtggtccatgttgtcaacttgt...

Basic information

species Oryza sativa
transcript LOC_Os05g28200.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 12
TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgttgcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgatt-atgtggtccatgttgtcaacttgt----
||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| |||||||| || | |||   ||    || | |   || |  | ||||      |||||   |  | ||||  | |  | | |  || ||       || || | |||     
TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaagg-catctgttgc--ttttttcctttataatacaaat-ccgccttcacttcaat-tcttactgtactagctcgatctgcataccattttctatttgccatg

upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA16G19390.1 (Glycine max), 5'ss of exon 4
TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgtt---gcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgattatgtggtccatgttgtcaacttgt
|| || || ||||||||||||   ||||||||||||||||||||||| || || |||||||| || |||||||| || || ||||||          |  | ||| |        ||  |  | | |  | |   |  | |  |   |  |  |  |  |||  |  ||  | |  |   |    
TCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTGgtaaattttgatccctcaaatatatacaaataattactatatatacaaacaaaacagttagaaacttttcaccatatttacttaatcattatccttgtcc---

upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA18G43310.1 (Glycine max), 5'ss of exon 12
-TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgtt-----gcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgattatgtggtccatgttgtcaacttgt
 || || || ||||||||||||   ||||||||||||||||| ||||| || || |||||||| || |||||||| || || ||||||          || | ||| |          ||| |  | | |  | |   |  | |  |   | ||  |  |  | |  |  ||  | |  |        
GTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATCTGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCGggtaaattttgttcccttaaatatatatacaaataattgctctatatacaaacaaaacagttagaaacttgtcaccatattcacttaatcattatccttg------

upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 12
TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgtt---gcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgattatgtggtccatgttgtcaacttgt
|| || || ||||||||||||   ||||||||||||||||||||||| || || |||||||| || |||||||| || || ||||||          |  | ||| |        ||  |  | | |  | |   |  | |  |   |  |  |  |  |||  |  ||  | |  |   |    
TCTCTTCCAGTTGCTTTTGGTTCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTGgtaaattttgatccctcaaatatatacaaataattactctatatacaaacaaaacagttagaaacttatcaccatatttacttaatcattatccttgtcc---

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|27547699|gb|CA765724.2|CA765724
EST:     GGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG                         GCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
genomic: GGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacat ... catttttcagGCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
EST: gi|88967759|gb|CI098001.1|CI098001
EST:     TTATCCGTTGCAG                         GCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
genomic: TTATCCGTTGCAGgtaaagacat ... catttttcagGCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
EST: gi|86494917|gb|CI137550.1|CI137550
EST:     AAAGTGGAAATGTGTAGGAGCGATTGACATAACTCCATTATCCGTTGCAG                         GCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
genomic: AAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacat ... catttttcagGCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
EST: gi|86906508|gb|CI294631.1|CI294631
EST:     AAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG                         GCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
genomic: AAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacat ... catttttcagGCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
EST: gi|86596619|gb|CI286532.1|CI286532
EST:     AAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG                         GCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC
genomic: AAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacat ... catttttcagGCTACCTTTTCAGTTCCGGCAAGCCTTATTATGCCCTGGCACTGCTAGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgttgcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgattatgtggtccatgttgtcaacttgt

- - - - - - - - - - - - - - - - - AGTGGA