Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atataaaatgtggactggtcaactatgaacatctgctgaaatcgtgttgtaaatcagtctaaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA

Basic information

species Oryza sativa
transcript LOC_Os01g02040.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G872442_T02 (Zea mays), 3'ss of exon 7
atataaaatgtggactggtcaactatga-acatctgctgaaatcgtgttgtaaatcagtc-taaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA
  |    ||   | |     || | ||| |  ||||  |||||  |  |     | |  | |   ||   |    || ||| ||   |||| | | |||||||||||||||||||||||  | ||  ||||||| |||||||  ||||||||| | ||| || ||||  ||||||||| ||| ||||  || ||||| || |
ggactgtatccag-ccctcgaagtgtgatatttctggagaaattataatactggtaaaccatgtggaccagcaatttttgtgaca-gcacagttatttgcagGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTGGTGGACGCCCGGCTTAACAAGAACTACAACGAAGTCGAGATGTTCCGTA

upper sequence: LOC_Os01g02040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G355636_T01 (Zea mays), 3'ss of exon 7
atataaaatgtggactggtcaactatgaacatct--gctgaaatcgtgttgtaaatcagtctaaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA
   | ||||     || |  || | ||    |    |   ||||  || ||   | || | |      |  ||  || |        |  | ||| |||||||||||||||||||||||  ||||  | ||||| ||||| | |||||||||| | ||  || ||||  | | ||||| ||||||||  |||||||| || |
tcttcaaatcccatctcg--aagtgtggtttttctggaaaaaataatgctggggaacaatgtgggccagcaattttttttgtgacagcgtagtcatttgcagGCTAGGCCATTGCTCACGCAAGCGCTCGAGACCGGCAATGCTGGGGAGCTGGTGGATGCCCGGCTTAATAGGAACTACAATGAAGTCGAAATGTTCCGTA

upper sequence: LOC_Os01g02040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G872442_T03 (Zea mays), 3'ss of exon 7
-------------------------atataaaatgtggactggtc----aactatga-acatctgctgaaatcgtgttgtaaatcagtc-taaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA
                          |||   |      |  | |    || | ||| |  ||||  |||||  |  |     | |  | |   ||   |    || ||| ||   |||| | | |||||||||||||||||||||||  | ||  ||||||| |||||||  ||||||||| | ||| || ||||  |||                              
tcattcactggttacattcaattcagtatgggactgtatccagccctcgaagtgtgatatttctggagaaattataatactggtaaaccatgtggaccagCAATTTTTGTGACA-GCACAGTTATTTGCAGGCTAGGCCATTGCTCACGCAGGCGCTTGAGACCGGCAACGCCGGGGAGCTGGTGGACGCCCGGCTTAACA------------------------------

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|86437136|gb|CI118858.1|CI118858
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGCCCATTGCTCACAGAAGCCATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86437496|gb|CI119218.1|CI119218
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|88197800|gb|CI197650.1|CI197650
EST:     GGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGGCTGGCAACGTTGGGGAGCTG
genomic: GGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86541720|gb|CI181926.1|CI181926
EST:     TGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: TGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87013927|gb|CI271318.1|CI271318
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGCCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87034702|gb|CI189326.1|CI189326
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGNCCATTGCTCACAGAAGCCATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87041394|gb|CI196016.1|CI196016
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|88234457|gb|CI234306.1|CI234306
EST:     TTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: TTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87024364|gb|CI274184.1|CI274184
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86858514|gb|CI273086.1|CI273086
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|66929099|gb|CX115947.1|CX115947
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|88197991|gb|CI197841.1|CI197841
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGGCTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86478718|gb|CI121351.1|CI121351
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87041598|gb|CI196220.1|CI196220
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87021491|gb|CI274098.1|CI274098
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86514733|gb|CI157366.1|CI157366
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGCCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86481600|gb|CI124233.1|CI124233
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86477444|gb|CI120077.1|CI120077
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCCAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|27576561|gb|CA999255.1|CA999255
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87021483|gb|CI274090.1|CI274090
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|89174423|gb|CI110621.1|CI110621
EST:     TTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGGCTGGCAACGTTGGGGAGCTG
genomic: TTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86483565|gb|CI126198.1|CI126198
EST:     GCCTG-TGACGGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: GCCTGTTGAC-GCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86481436|gb|CI124069.1|CI124069
EST:     AACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87021141|gb|CI271948.1|CI271948
EST:     AGCCTGTTGACGCATCTAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACGGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|87042014|gb|CI196636.1|CI196636
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86518528|gb|CI158734.1|CI158734
EST:     GCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: GCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86525079|gb|CI165285.1|CI165285
EST:     ATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: ATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86480472|gb|CI123105.1|CI123105
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGCCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
EST: gi|86436777|gb|CI118499.1|CI118499
EST:     AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGG                         GCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG
genomic: AGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 63 (downstream exon)
Score: 6

TGATGTATTCTCTTTTGGCGTTGTTCTCTTAGAGCTTATTACCGGTAGAAAGCCTGTTGACGCATCAAAACCATTGGGTGATGAGAGCCTTGTTGAGTGGgtaagctata ... tcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtaaatcagtctaaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA
                                  aacttac  putative branch site (score: 6)
                                 taactta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atataaaatgtggactggtcaactatgaacatctgctgaaatcgtgttgtaaatcagtctaaagaggggatccttgtgtaacttacacaatcacttgcagGCTAGGCCATTGCTCACAGAAGCAATTGAGACTGGCAACGTTGGGGAGCTGATTGACTCCAGGCTGGACAAGAACTTCAATGAAGCTGAAATGTTTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - atgaaca
- - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - cgtgttg