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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaggttaaattatttacttagcctgtcaaactaccaatgtttgagatattaagccctttacccaccccctaatcatcgttttattttgaaaattgtcagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAGGTGCATATATTACATCAATGTGTCCTTCAGTATTTCAGTT

Basic information

species Oryza sativa
transcript LOC_Os03g22430.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G030072_T03 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------caaggttaaattatttacttagcctgtcaaactacc--aatgtttgagatattaagccct--ttacc-caccccctaatcatcgttttatt-----ttgaaaattgtcagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAGGTGCATATATTACATCAATGTGTCCTTCAGTATTTCAGTT
                                                                               || | |    | |||    ||| || | |     |   |   ||||    ||   | | |  || |   |    | |||  |  ||| |||     |    | ||||||||| || |||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||                                        
gtaagcaagattgttcaattggtgacttcagtcaagtatttccagtattggggtcagtaccggtagaatttggcttattcatgttcttctaattagggtagactataaggtctctttagcatttgtatcatgtcgtcatggttgctatatagtcaaatagttctttaattgattgtctgtatttgtcagGTCGGGATGGAGAGCGAAGGTTTTGCAATCTATGATGCAATGATGCGTATGAAAACTGAG----------------------------------------

upper sequence: LOC_Os03g22430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G39570.1 (Glycine max), 3'ss of exon 3
---------------------------------------------caaggttaaattattt---acttagcctgtca--aactaccaatgtttgagatattaagccctttacccacc-----ccctaatcatcgttttattttgaaaattgt------cagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAGGTGCATATATTACATCAATGTGTCCTTCAGTATTTCAGTT
                                                ||| |  ||||||   | ||    | ||   |  |    ||  |  |   |||||||    |  |  ||     || |  | ||| |  |   ||   | || |      ||||| || ||||||| |||||||||||| || |||||||| ||||||| | ||||||  |||                                        
gtaattggcttctggcttactgtttatatgaaaatttttatttgctgtggtcactttattttgcattttttatatctgtagtttaagataatctatgaattaagctgcctctctgcctttgtcctttgttatcctcatgccttttgagttcttgcattcagGTAGGCATGGAGACTGAAGGTTTTGCCATTTATGATGCAATGATGCAGTTGAAAAACGAG----------------------------------------

upper sequence: LOC_Os03g22430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0060g02160.t01 (Vitis vinifera), 3'ss of exon 3
-----caaggttaaattatttacttagcctgtcaaactaccaatgtttgagatattaagccctttacccaccccctaatcatcgttttattttgaaaattgt-cagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAGGTGCATATATTACATCAATGTGTCCTTCAGTATTTCAGTT
          |  |  |||| | ||| | | |    | | |||| | |   | |||||    |||| ||  |   |   ||| | || |  |||    |||| |||||||| ||||||| ||| |||||||||||||||||||| ||||||| | | |||| ||||                                        
tgttgtgttctagagctattcatttaactttttgggc-atcaatttatactacattaa---ttttaaccttctgtt--ccatgggttcaaattgtttgttgttcagGTTGGGATGGAGACTGAGGGTTTTGCTATCTATGATGCAATGATGCAGTTAAAAAATGAG----------------------------------------

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|3760393|gb|C97647.1|C97647
EST:     TTTACATATACATCAACTCCACAGGAACAGCTCGTGATGATGGTGAACCA                         GTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATG
genomic: TTTACATATACATCAACTCCACAGGAACAGCTCGTGATGATGGTGAACCAgtaagcatgc ... aaattgtcagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattaagccctttacccaccccctaatcatcgttttattttgaaaattgtcagGTTGGAATGGAGAGTGAAGGTTTTGCTATCTATGATGCCATGATGCGGATGAAAACTGAGGTGCATATATTACATCAATGTGTCCTTCAGTATTTCAGTT
                      ccctaat  putative branch site (score: 3)
                                  ttttattttgaaaatt  TA-rich tract