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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattcttattctatatccatgtcttcctttttccaaatgttataatgtagatagttgactgcagatactagaactgtataattaaacttctgtggtgttgacag

Basic information

species Oryza sativa
transcript LOC_Os02g47600.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 4
ATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattcttattctatatccatgtcttcctttttccaaatgttataatgtagatagttgactgcagatactagaactgtataattaaacttctgtggtgttgacag
||||| || ||||||||||||||||||| ||| |||| || |||||||| |||  |||| || || ||||||||||||||||||||||| |||||||| ||||| ||||||  || ||||||   |||     | || | ||||| |||  ||||  |  | |||||  ||||||     ||  |||   |||||  ||||||||||
ATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGATCCGCCGCTTTTTTGAAGATTgtatgttcttaaactgtatccacagcttg----tccccagtgttacaatccagatcataaaatgcagtaactagagtccaatcgttatgtttctgccgtgttgacag

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 7
ATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattcttattctatatccatgtcttcctttttccaaatgttataatgtagatagttgactgcagat-actagaac--tgtataattaaacttctgtggtgttgacag
||||| |||||||||||||||||||| | |||||| | ||  |||||||||||  | || || || || |||   || ||| |  | |||||||| ||||||||  | ||||| |  |   ||   |         ||    |     |     |  |||||     || | |||     | || ||| || | | |     ||      
ATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAATCAGAAGATTCTTTGAGGACTgtatcctgttatt-tgcacttatacataaacc---acatgcatctctgtacgagttattgacaattaatgattagtttcttttacaataaagcctatagaacgt------

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 6
ATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtat--------attcttattctatatccatgtcttcctttttccaaatgttataatgtagatagttgactgcagatactagaactgtataattaaacttctgtggtgttgacag--------------------------------------------------------------
||||| || ||||||||||||||||| | |||||||| ||  |||||||| || || ||||| || ||||||   |||||||||||||||||||| ||||||||        || | | | ||   |  || | |  ||| || | | |  || | |    ||  || | | |  ||||   || ||| |   |||  | ||      ||||||                                                               
ATAGCAGTGTGTGCTGATGACCCTGAGTTCCGCCACTACAAAGACATCAAAGAGATTCCCCCACATCGCCTTGCTGAGATCCGCCGCTTCTTTGAGGACTgtatccattcacatgcctttactccttttatatataacttgttgctagtcatagactcacaattatttaatact-atacataaattgttttcctaag-tgctaccaaattgacatgttttttggtgaatttacattatctattactggataaccttcactccccatgaatgacaaag

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|86522195|gb|CI162401.1|CI162401
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|163918159|gb|EG715273.1|EG715273
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|33823831|gb|CF337722.1|CF337722
EST:     CACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: CACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|163926919|gb|EG715144.1|EG715144
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|8404630|gb|AU091984.1|AU091984
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|16753343|gb|BM037722.1|BM037722
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|15852955|gb|BI805751.1|BI805751
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAAC-AAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|8858737|gb|AU096055.1|AU096055
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|33663640|gb|CF294607.1|CF294607
EST:     GAAATNNNNNNNTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GAAAT-CCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88503068|gb|CI430574.1|CI430574
EST:     TTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: TTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|58689221|gb|CK077908.1|CK077908
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|40487599|gb|BX898545.1|BX898545
EST:     CCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: CCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|33662651|gb|CF293618.1|CF293618
EST:     CAAGAGATCCGCCGCTTCTTTGAAGACT                         CCAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: CAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88988638|gb|CI039057.1|CI039057
EST:     CCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACCAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: CCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|8404547|gb|AU091901.1|AU091901
EST:     CCGCTTCTTTGAAGACT                         ACAGGAAGAATGAGNNCCAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCA
genomic: CCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAG-AACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCA
EST: gi|163928605|gb|EG710890.1|EG710890
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88470644|gb|CI407915.1|CI407915
EST:     AGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: AGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88250322|gb|CI348552.1|CI348552
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88256927|gb|CI354708.1|CI354708
EST:     TCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: TCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88663129|gb|CI476747.1|CI476747
EST:     GCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88984805|gb|CI009553.1|CI009553
EST:     GAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|58596788|gb|CK007316.1|CK007316
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88256729|gb|CI359117.1|CI359117
EST:     GATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|88490240|gb|CI427512.1|CI427512
EST:     CACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: CACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
EST: gi|86251686|gb|CI018283.1|CI018283
EST:     GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG
genomic: GGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattctt ... gtgttgacagACAAGAAGAATGAGAACAAAGAAGTTGCTGTCAATGAGTTTCTCCCAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGATCCGCCGCTTCTTTGAAGACTgtatattcttattctatatccatgtcttcctttttccaaatgttataatgtagatagttgactgcagatactagaactgtataattaaacttctgtggtgttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA