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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtgctattttactggtttctcctgtgcttaatttctctctgcatagagtggatgataaaaccttcctgaagtcaatcgacccatgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC

Basic information

species Oryza sativa
transcript LOC_Os01g64780.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 6
gttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtgctattttactggtttctcctgtgcttaatttctctctgcatagagtggatgataaaaccttcctgaagtcaatcgacccatgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC
                                                                                | |  || |||| |   ||| |     || | ||| ||       | | |||     | ||  |      |||  |||  || | | ||  |  |  || ||  |  | ||||||||||||| || ||||||||||| ||||| |||||||| || || || || ||||  ||| |||| |||||||| || |||||||||||||| | |  
--------------------------------------------------------------------------------tccccaacttctgtagacatggc-caaataacaaatcc-------atttaattattgcttgcta----ggattgataaaccaatatattattcattcttttggtttctgcagAAATAATTGTGTCAGGAGGAATGACCATGCCTCAGGTGATTGCATCACTGGAGCCCATGCCACGGAAAAGCCAGAACATTCGTCTAAATAGAATGACGTG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G046098_T05 (Zea mays), 3'ss of exon 6
gttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtg-ctattttactggtttctcctgtgcttaatttctctctgcatagag-----tggatgataaaaccttcctgaagtcaatcgacccatgtaatt--cta-aatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC
    ||       | | | | || |  |  ||   |   | |||||      ||||||| | | ||| || |    || |||   |  ||| |  ||   |||       || || | ||||   |   |||  ||    | |  | |   |  ||| ||||  |||  || | | ||  |  |  || ||  |  | |||||||||||||||| ||||| ||||| ||||| |||||||| || || || || ||||  ||| |||| |||||||| || |||||||||||||| | |  
----gtatggtagtttggttaatatgatgcctagcatctctatattattatgtcatgtggcaactttccttgaaattcttgttacttgttttttcctatctagtcaattttgcattacaaaaaacttacgaatccatcgaatcattattgcttgctagaattgataaatcaatatattattcattcttttggtttctgcagAAATAATTGTTTCAGGAGGGATGACCATGCCTCAGGTGATTGCATCACTGGAGCCCATGCCACGGAAAAGCCAGAACATTCGTCTAAATAGAATGACGTG

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 6
gttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtgctattttactggtttctcctgtgcttaatttctctctgcatagagt--ggatgataaaaccttcctgaagtcaatcgacccatgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC-
                                                                                   |||     |    |  | |  |  | ||| | |||  ||| | || |  ||         |  |||||| ||| |  |   ||   | ||||||  | |||    || ||||||| |||||||| ||||||||||||||||||||| ||||  |  |  | |||     | |  |   ||   | |   ||  | | || |||||   ||  
-----------------------------------------------------------------------------------ttagaactttgtcgtttggcttctgcatgttgaaa--ttcttaaaat--attattttcatttcttctaattttatggt---gtacatgtcttttgatgctg----atgcagAAATCATTGTTTCCGGAGGAATGACTATGCCACAGTTGATATCTCCAGTGGAAAGGGACACTCGACCGAATGAAAGAGTCTCTTTGAACAGAATTG-GATA

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|88844233|gb|CI005606.1|CI005606
EST:     GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
genomic: GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
EST: gi|29626495|gb|CB631506.1|CB631506
EST:     GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
genomic: GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
EST: gi|33681466|gb|CF309705.1|CF309705
EST:     GAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
genomic: GAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
EST: gi|88429235|gb|CI690129.1|CI690129
EST:     GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
genomic: GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
EST: gi|8856716|gb|AU094034.1|AU094034
EST:     AACTCTGAGGAGATAATAAGNCCCAAATTTATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATNCCACAGGTGATCGCGTCCCTTG
genomic: AACTCTGAGGAGATAATAAG-ACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
EST: gi|86255848|gb|CI068297.1|CI068297
EST:     GAGGAGATAATAAGACCAAATTAATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
genomic: GAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
EST: gi|88981799|gb|CI027377.1|CI027377
EST:     GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCG                         AAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG
genomic: GAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTG

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: 73 (upstream exon), 53 (downstream exon)
Score: 22

AGCGTTTATGTGCCAACAAATCATCTTTACATTGGTGACATATTTCTGGTGAACTCTGAGGAGATAATAAGACCAAATTTATCCATTCGAGAAGGAATCGgttggttctc ... catcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC
               ttctaat  putative branch site (score: 22)
                          tgtttttcttttcttt  putative PPT
     aattctaaatttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttctcctatcttgcttatgtactatctcctactgcaatattgcatgatcatgtgctattttactggtttctcctgtgcttaatttctctctgcatagagtggatgataaaaccttcctgaagtcaatcgacccatgtaattctaaatttctaatacagtgtttttcttttctttctgcatcattcagAAATAATTGTTTCTGGAGGAATGACTATGCCACAGGTGATCGCGTCCCTTGAACCCACCCCAAGGAAGAGCCAGAATATCCGTCTAAATAGAATAATGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA