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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

Basic information

species Oryza sativa
transcript LOC_Os05g32110.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   |||  ||    |||    |  | ||  ||          ||| |  | || | || ||    |      | ||||||||| | | |   | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||||||||||||||
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtc-tagattttatagcagaga--gggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   |||  ||    |||    |  | ||  ||          ||| |  | || | || ||    |      | ||||||||| | | |   | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||                              
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtc-tagattttatagcagaga--gggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgt---ttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
 |  || |  |      |   ||  ||||||    | |  ||  |   |    |  |||||       ||    ||||||||| | ||    | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattc--tttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgt---ttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
 |  || |  |      |   ||  ||||||    | |  ||  |   |    |  |||||      |||    |||||| || | ||    | | | |||||||||||||||||||||||||||||| |||||||||||||||||||||||||  |||||||||||||||||||||||||||||||||||||||||||||||
-ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgtctatattttatagcattgagagttcttatcagacattc--tttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttg--tcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  ||||  || || | ||| |   |   | ||  |    |  |  ||| |  ||| | |||     |  ||||   |||||||    |   || | || |||||||||||||||||||| |||||||| || ||||||||||||||||  || ||    |||||||| || |||||||| || |||||  | ||| ||||   
-ccatacgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgac-cttaacattgctctgatttatt-gcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATAACAATACAGTTGTACC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttg--tcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  ||||  || || | ||| |   |   | ||  |    |  |  ||| |  ||| | |||     |  ||||   |||||||    |   || | || |||||||||||||||||||| |||||||| || ||||||||||||||||  || ||    |||||||| || |||||||| || ||| |  | ||| ||||   
-ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgac-cttaacattgctctgatttatt-gcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA----------------------------------------------
                                        |  ||  || ||   ||  |||   ||| |   |||||     ||| |   | || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| ||  | ||| |||  | ||||||||| || |||||  | ||||| || ||                                              
---------------------------------------ttattagtatgaaacccaagttttggtttag---cttaatctgcatata--tttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
--atc--atagtggctccatatagaagttaaattt-gtcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  |||  | |  ||  | |  ||  ||||    |  ||    |  |  ||| |  ||  | |||     |  ||||   | |  |     |   || | |  ||||||||||||||||| || |||||||| || ||||||||||||||||  || ||    ||||| || || || ||||| || ||||| || ||  ||||   
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgc-----tctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
-atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttct-taacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
  | | | |     ||  |  |  ||| | |||  |  |     || || ||| ||| |     |||  | | ||  |||||  | |    | | || |||||||||||||||||||| ||||||||||| |||||||| ||||| || ||||| || || ||||| || || ||||| || |||||||| ||  ||||   
gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattc-tggcaatttactatatccataacatcactcttgtttatt-gcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
atcatagtggctccatatagaagttaaatttgtcaaaatctt--ataccataaagttcatttttgttttttgttt--cttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
   ||    |||  ||| |    | | ||   | |  |   |  | |||||    |   ||||    ||| ||||  |||||     ||| |   | || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| ||  | |||||||| ||||||||||| || |||||  | ||| | || ||
--tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatata--tttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
---atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaat-ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
    | | | |     ||  |  || ||| | |||  |    | | || |    || | ||| | |   | ||||   |    || || |  |  | ||||||||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| || || ||||| || |||||||| ||  ||||   
gtgcttaaatttaaaacaactgaaaattacagttggta----cctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
----atcatagtggctccatatagaagttaaatttgtcaaaatcttataccata---aagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
     | |    |       |    |   |||    |   | | ||     | |   ||  | | |||||  |||| ||| |   |    |             ||||||| |||||||| || ||||||||||| || ||  | |||||||| || ||  | |||||||||||||| ||||| ||||||||  | ||||| ||   
gtaagttactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtga-------------cagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttg---cagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
     ||||  ||   |  | | ||    |  ||   |  | | |   | |  |  |||     |   |||       | ||| | |  ||| | ||   |||||||||||||||| || ||||| || || ||||| ||  ||||||| || ||  | |||||||| || |||||||| || || ||||||||||||||   
-agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagct--attacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC

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|66918925|gb|CX105773.1|CX105773
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|58686271|gb|CK074958.1|CK074958
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAGCCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|58654342|gb|CK043022.1|CK043022
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|33676440|gb|CF304679.1|CF304679
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|58660640|gb|CK049320.1|CK049320
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
EST: gi|29684532|gb|CB680807.1|CB680807
EST:     GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAA                         TGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC
genomic: GCCTACTAAGTTTTTCACCGGGGATGGGCGCAGAGCAACCCAAGCTCTAAgtaagtagct ... ctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
                           tcttaac  putative branch site (score: 2)
                                            tctgttt  putative PPT
        ttcatttttgtttttt  TA-rich tract