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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os07g37610.1
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008356_T01 (Zea mays), 3'ss of exon 4
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
|||||| | | ||||||  ||| || || || ||||| |  | |   || ||  ||   |||| |  | |  ||  ||    |  | | || ||  |||| ||||||         || ||| ||| ||||||  || ||||| ||||||||||||||||| ||||||||||| || ||| ||||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||
gtatccgacacattctacttatgttaataagtaattttccttggc--at-tactttctgtagtcataattcccaacttccatagatatgttattc-gtttgaactcta--------ttgagt-tttacttaactttcaaacagTTCAAATTCTGTTATTACTCCTTTGTTTGAAAAGATGCTAAGTGCTAGTGATGCTGGGCGGATTGGTCGTTTAGTTTTGCCAAAGAAGTGTGCTGAG

upper sequence: LOC_Os07g37610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G31970.1 (Glycine max), 3'ss of exon 5
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
                  ||||| |    | ||| |   | |||    | | | ||||    ||| || | | |||    |    | |    || ||| |||   | | |  |    ||     | |||||||  |    ||| ||||||||||| ||||| || |||||| ||||||  || ||||||||||||||||| || ||||| ||||| ||| | || ||||| |||||||||
------------------gtatccttcaaatcaaatgattgtag----tgttggtttatatataactatt-ttattgcacttcgttttccaattatgtctaatgccatactggaagcta--caataccttaactttatcccagTTCAAATTCTGTAATTACTCCCTTGTTTCAGAAAACTTTGAGTGCTAGTGATGCTGGGCGAATTGGGCGTTTAGTGCTACCCAAGAAGTGTGCTGAG

upper sequence: LOC_Os07g37610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G07350.1 (Glycine max), 3'ss of exon 6
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
                  ||||| |  |||  |||  | |     || |   | ||||    ||| || | |  |    ||||  | |       ||| |||   | | |  |    ||     |  ||||||  |    ||| ||||||||||| ||||| || |||||| ||||||  || ||||||||||||||||| || ||||| ||||| ||| | || ||||| |||||||||
------------------gtatcct--tca--aatcacatgatcgtagtgctggtttatatataactattttattgcacttcat-tttccaagaatgtctaatgccatactggaagcta--caatatcttaactatatcccagTTCAAATTCTGTAATTACTCCCTTGTTTCAGAAAACCTTGAGTGCTAGTGATGCTGGGCGAATTGGGCGTTTAGTGCTACCCAAGAAGTGTGCTGAG

upper sequence: LOC_Os07g37610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0181g00260.t01 (Vitis vinifera), 3'ss of exon 5
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
                 || |  ||||| || | ||| || || ||||| |||||  |     |||| |       | ||  ||       ||| | |||| | | | || |  | |  |      |||||||| |     || ||||||||||| || || ||||||||||| || ||| ||||||||||||||||||| || || || ||||| ||| ||||||| ||||||||||||
-----------------tgaagattcattag-agtttgctttatataat-tagatgca-----aaatgc------ctgttgaac-------tttctatttacaatttagcatcctataga------ccttaaccatgtgtaagTTCAAATTCTGTAATCACTCCTTTGTTTGAAAAGATGCTAAGTGCTAGTGATGCTGGGCGTATAGGGCGTTTAGTGCTGCCAAAAAAATGTGCTGAG

upper sequence: LOC_Os07g37610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S31_242V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactg-tcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctcca--acagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
                  ||||| |    |  | |||      | | ||  | ||||    |||||||  | | |     ||||   ||   |||    |   | |     ||  |||| ||| ||  ||| ||  | ||  ||||| || |  ||   || || ||| |||| ||||||||| | ||||| |||||||| || |||||||||||||||||| | |||||   ||| || |||
------------------gtatcctttcta--agttt------gtttattcaaatttgt--gtaaataggggttacgggattca---gtgagtttcgagtatcattacaatctaatcttcagttttcacttgacaatgcattacagCACACAAACTACCATCACTCCTCTGTTCGAGAAAATGCTGAGTGCCAGTGATGCCGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGCGCCGAG

upper sequence: LOC_Os07g37610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S42_132V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatata-gatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaac--agCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
                  ||||| |  ||||  ||||| |  |   ||| |  |||||  | | |     ||    |||||     | || |  |||  |||||    | |    | | || ||| | ||| ||  |  |    ||     |  |    || || || ||||| ||||||||| | ||||| || |||||||| |||||||||||||||||| | |||||   ||||||||||
------------------gtatcctt-tcag--atttcatgcattcaatttctgatttcgtggga-----tgagggtttttgggatttttatgattttcttaaaagggtac--agtttaaattgtgtacttgacaatgtattttagTATGCAAACCACCATCACTCCCTTGTTCGAGAAAATGCTGAGTGCCAGCGATGCTGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGTGCTGAG

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|58663255|gb|CK051941.1|CK051941
EST:     CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGA                         CTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
genomic: CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGAgtatccaaaa ... cctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
EST: gi|58662796|gb|CK051482.1|CK051482
EST:     CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGA                         CTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
genomic: CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGAgtatccaaaa ... cctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
EST: gi|58668424|gb|CK057110.1|CK057110
EST:     CGCTATTGGCCTATAATAACAGATCAAGAGCTACAGCACCTATCTGGAGA                         CTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
genomic: CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGAgtatccaaaa ... cctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
EST: gi|33677354|gb|CF305593.1|CF305593
EST:     CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGA                         CTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
genomic: CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGAgtatccaaaa ... cctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
EST: gi|29681679|gb|CB677954.1|CB677954
EST:     CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGA                         CTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA
genomic: CGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGAgtatccaaaa ... cctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGA

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: 58 (upstream exon), 55 (downstream exon)
Score: 16

GCAATGGAAGGCCTAGAATGGATGCAAAGGCGAGATCTCAGTTGCTTCCACGCTATTGGCCTAGAATAACAGATCAAGAGCTACAGCACCTATCTGGAGAgtatccaaaa ... cctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG
 ttccttaac  putative branch site 
                                   tttccttaaccctcc  putative PPT
     tttgtttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccaaaaaattctatgtatcttcatcagcaatttcctctagataatatagatttactagtaaatactgtcatttttttcacgtgtttttttttgtttaaactcttgcctgttcttaagtgtttccttaaccctccaacagCTCAAATTCTGTTATTACCCCTTTGTTTGAGAAAATGTTAAGTGCTAGTGATGCTGGACGGATTGGTCGTTTGGTGTTGCCAAAGAAATGTGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA