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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG

Basic information

species Oryza sativa
transcript LOC_Os05g30800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G467059_T03 (Zea mays), 3'ss of exon 2
-tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttt--tctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
      |      || || | |  |  | ||  | |||| |||| |||| | | |  ||||| || || ||| | | | |      |||     ||||||||||||||||||||| ||||| ||||| || || |||||||| || ||||||||||| ||||| ||||| ||||||||||| |||
acagactcacttgcatctgtagtat--taatgaataattgttttaactctgttgtattctgtaggaaaacaagt-atgttgagatttttttccccttttacagGCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G033626_T01 (Zea mays), 3'ss of exon 2
--tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttt--tctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
  |        |   | | ||       |||   |  ||| |||| |||||| | |  ||||| || || |||||      ||||| ||||    ||||| ||||||||||||||| ||||||||||| || || |||||||| || || |||||||| ||||| || || ||||||||||| |||
tgtggaaaacccactagcattcatagtattaatcaatattgttttaactcagttatattctgtaggaaaacaaat---atgtgata-tttccccccttttgcagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G033626_T04 (Zea mays), 3'ss of exon 2
--tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttt--tctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG------------------
  |        |   | | ||       |||   |  ||| |||| |||||| | |  ||||| || || |||||      ||||| ||||    ||||| ||||||||||||||| ||||||||||| || || |||||||| || || |||||||| ||||| || || ||||||||||| |||                  
tgtggaaaacccactagcattcatagtattaatcaatattgttttaactcagttatattctgtaggaaaacaaat---atgtgata-tttccccccttttgcagGCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAGGTCTATGCAAATCCACTT

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 2
tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttttctgtgggcaagcaaattaagcttgataatttcgttgctt-----ttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
 ||  |  |       |  ||| |    |   |   | || | |||  |  | |        | ||  || | | ||||||   |  |||| ||      | ||| ||||| |||||||| || ||||||||||| ||||| || |||||||||||| | || || || || ||||||||||| |||
-ctacttatatttgattcatgcgtaa--actgaacgtgatgtgtacgaatatgtctaaaatactag--aaatcaccttgatgcctgtgttgtttgtgttctgcagACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 3'ss of exon 3
--tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
  |   |  ||      |  |||       ||    |  | |   ||   | | | |||     |  |    |  |  |  ||   || ||    ||| ||||||||||||||| || || ||||| ||||| ||||| || |||||||||||| | || || || || || ||||||||||||
gttgaatgtgtgagtgtcagttgtgaataaattctcagatttaactatgaatcatatctagattccggtg--tgcatttaaattgctttgtgcacttttcagGCCAGAAATGGTTGTGGGCTGGTATCATTCACATCCAGGTTTTGGTTGCTGGTTATCTGGTGTGGATATAAATACTCAACAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ33925 (Selaginella moellendorffii), 3'ss of exon 2
tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
                                     ||   |  || | ||||    ||| ||  |   ||      ||| ||||     ||  | ||||   |||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||||| || || || 
------------------------------------gtacgctagctaaactttggattggacac-cgcgttttctcagattatttt----ctgctccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ16494 (Selaginella moellendorffii), 3'ss of exon 2
tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
                                       || |||      |||||| |   |  |     |     ||  || ||      |||| |||  | |||||||| ||||| ||||| ||||| ||||||||||| || ||||||||||| |||||||| |||||||||||||||
--------------------------------------gttcttatcacatttttcttttctcttgtgggattcaagtgtgaagtt------ttttgcagATCGGAAATGGTTGTAGGATGGTATCATTCACATCCTGGATTCGGGTGCTGGCTTTCTGGAGTTGATATCAATACTCAACAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 2
tctgttggtcgacaccttttgcttggttatctagaattatttttactc-agcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
                                           ||| | ||||   || |||       |  |    ||   |  ||  || ||  | ||||   |||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||||| || || || 
------------------------------------------gtacgctagctaaactttggattgaacacctcgttttctcagattattttctactccagGAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAA

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|29615551|gb|CB620563.1|CB620563
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|58599931|gb|CK010459.1|CK010459
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|58681730|gb|CK070417.1|CK070417
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|33682841|gb|CF311080.1|CF311080
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|58686484|gb|CK075171.1|CK075171
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|88826224|gb|CI776789.1|CI776789
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGTTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTG
EST: gi|15008261|gb|AU222649.1|AU222649
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|29620645|gb|CB625656.1|CB625656
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|218498489|gb|FG961937.1|FG961937
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG
EST: gi|117227458|gb|CT846600.1|CT846600
EST:     GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAG                         GCCAGAAATGGTGGTAGGCTGGTACCATTCCCATCCTGGATTTGGTTGCTG
genomic: GACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTG

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), 72 (downstream exon)
Score: 25

ACGTCTTCGCCATGCCGCAGAGCGGGACCGGGGTCAGCGTCGAGGCCGTCGACCATGTCTTCCAGACCAACATGCTCGACATGCTCAAGCAGACCGGGAGgtaataatgc ... gcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG
                             gcttgat  putative branch site (score: 25)
                                           ttgctttt  putative PPT
                               ttgataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttggtcgacaccttttgcttggttatctagaattatttttactcagcttttctgtgggcaagcaaattaagcttgataatttcgttgcttttacagGCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG

-ctgttgg
- - - - - - - - - ttgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaagca