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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatttgcgggacttctatttagagttttagaccactcttaacttccactcaagtttatcagttatgctaatttcttttcctagatcttt...

Basic information

species Oryza sativa
transcript LOC_Os01g44310.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G316635_T03 (Zea mays), 5'ss of exon 5
AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatttgcgggacttctatttagagt-------tttagaccactctta-acttccactcaagtttatcagttatgctaatttcttttcctagatcttt
||| | |||||||  ||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||  |  |||   ||    |||||||||||  |         | | |   ||| |   |||||||||     |||||||  |  || ||  |  |   |||      
AGACTGGCTGAATTTCTTGATCCTGAAGTCAAGAGATGGTCAAATGGAAAAGAAGGAAATCTGCGAGCATTGCTGTCCACATTGCAATATgtacgtgttttggcttatatgacttctatttgaaccatgtacatcttggttactgtaggacttccactggttcttatcag--aaacttatgcccatcattag------

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G316635_T01 (Zea mays), 5'ss of exon 5
----------AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatttgcgggacttctatttagagt-------tttagaccactctta-acttccactcaagtttatcagttatgctaatttcttttcctagatcttt
          ||| | |||||||  ||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||  |  |||   ||    |||||||||||  |         | | |   ||| |   |||||||||     |||||||  |  || ||  |  |   |||      
TTGGATACAGAGACTGGCTGAATTTCTTGATCCTGAAGTCAAGAGATGGTCAAATGGAAAAGAAGGAAATCTGCGAGCATTGCTGTCCACATTGCAATATgtacgtgttttggcttatatgacttctatttgaaccatgtacatcttggttactgtaggacttccactggttcttatcag--aaacttatgcccatcattag------

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G25190.1 (Glycine max), 5'ss of exon 8
AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatt-tgcgggacttctatttaga-gttttagaccactcttaacttccactcaagtttatcagttatgctaatttcttttcctagatcttt
|||||||| |||  ||| ||  | ||||||| ||| ||||||| |||||| ||||||||| |||| ||||| || || || ||||||||||||  |  || |||| ||    |  || | | |    |      ||  ||||  ||| | | ||| ||  |   | |  | |   | |       ||  |||
AGATTAGCAGAAACCCTGGATACTGAAGTCAGGAGGTGGTCAAGTGGAAAAGAAGGAAATTTGCGTGCATTACTTTCAACCTTGCAATATgtaggtttttgtattctgaaataagtcaaataactcatgcccctcctttcttctcttacccccaacttcttt--tcactcaacactgtaaggggtgacattt

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G06160.1 (Glycine max), 5'ss of exon 13
AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatttgcgggacttctatttagagttttagaccactcttaacttccactcaagtttatcagttatgctaat--ttcttttcctagatcttt
|||||||| |||   || ||  | ||||||  ||| ||||||| |||||| |||||||| ||||| ||||| || || || ||||||||||||  |  |||| | | | | | |   |  |     |     |  |||||| ||   | |    ||||      |   |||   |    ||   || ||   
AGATTAGCAGAAACTCTGGATACTGAAGTCCGGAGGTGGTCAAGTGGAAAAGAAGGAAACCTGCGTGCATTACTTTCAACCTTGCAATATgtaggt--ttttgtattctgaaataacacatgtcactcctttcttctcttagctgtaatttctttttactcaacactgtaagggtgacatttgaaggtccac

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv04s0023g02070.t01 (Vitis vinifera), 5'ss of exon 6
AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatttgcgggacttctatttagagttttagaccactc-ttaacttccactcaagttt-atcagttatgctaatttcttttcctagatcttt--
|| ||||| |||    | ||  | || |||||||||||||||| |||||| ||||| || ||||| |||||||| || |||||||||||||||| |      ||       | | |  |    | | ||       |  || |  |   ||| | ||  || |  |||| |     |  || | |  | | |  
AGGTTAGCAGAAACTTTGGATGCTGATGTCAAGAGATGGTCAAGTGGAAAAGAAGGGAACCTGCGTGCATTGCTTTCAACATTGCAATATgtaagtgtgaccatgatgtttaatgcattgcgaactattgtggtgtttgttgatatgacctctacttggataaaatatgatg----cactttcaaagtttctat

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|33653814|gb|CF276428.1|CF276428
EST:     CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATAT                         ATCCTTGGTTCAGATAATGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
genomic: CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatactt ... ttcctggcagATCCTTGGTTCAGATAATGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
EST: gi|58680897|gb|CK069584.1|CK069584
EST:     CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATAT                         ATCCTTGGTTCAGATAGTGGTTGGCCATCGGTTCCCCTCACAGATCTCATT
genomic: CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatactt ... ttcctggcagATCCTTGGTTCAGATAATGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
EST: gi|29617071|gb|CB622083.1|CB622083
EST:     CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATAT                         ATCCTTGGTTCAGATAGTGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
genomic: CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatactt ... ttcctggcagATCCTTGGTTCAGATAATGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
EST: gi|58589020|gb|CF987328.1|CF987328
EST:     CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATAT                         ATCCTTGGTTCAGATAGTGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
genomic: CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatactt ... ttcctggcagATCCTTGGTTCAGATAATGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
EST: gi|29621424|gb|CB626435.1|CB626435
EST:     CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATAT                         ATCCTTGGTTCAGATAGTGGTTGGCAATCGGTTCCCCTCACAGATCTCATT
genomic: CAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatactt ... ttcctggcagATCCTTGGTTCAGATAATGGTTGGCAATCGGTTCCCCTCACAGATCTCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATTAGCTGAATACCTTGACCCCGAAGTCAAGAGATGGTCAAATGGAAAGGAAGGAAATCTGCGAGCATTGCTATCTACATTGCAATATgtaaatacttttatttgcgggacttctatttagagttttagaccactcttaacttccactcaagtttatcagttatgctaatttcttttcctagatcttt

- - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA