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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttactcttgagcaaagattccctcttttctctggagcgttctgagttgcctattcttgtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g56580.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 13
--gtactctt-actcttgagcaaag-attccctcttttctctggagcgttc-tgagttgc------ctattcttgtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG
   |  |||  | |||   ||| ||   |   |||   |   |   | ||  | || | |      || |||||| ||||| ||||||||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||  ||||| |||||||||||||||||||||||||
gtatggtctcgattctcatgcatagtgctttttctaagcaaggctacatttataagctacaagtgtcttttcttgcacttt-agGATTGGATTATGGAGCAGTGGGAAAATAACTACTACATCAGTGCCATAGCTGGTGCAATGAATGGGAGTTCCTTGGTGGTCATGTCAAAAG

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 13
------------------------------------------gtactcttactcttgagcaaagattccctcttttctctggagcgttctgagttgcctat-tcttgtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG
                                            |    |||   ||||  || |||   |  ||  | |   | || ||| | |||     | |||  || | |||| |||||||||||||| |||||||| |||||||| |||||| | ||||| || |||   ||||||||||||||||| |||||||| ||||
gtgggttttttcttccttgatttatataattcatcttttgttaaataaatacgtatgagttaa-attaaataattgatgtcttg-gtgctgggctgctggcattttgatctctcagGACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAG

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 13
-gtactcttactcttgagcaaagattccctcttttctctgga-gcgttctgagttgcct-----------------attcttgtacttt---tagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG
  || | ||  || || |   |  |    | | |||| ||   | ||||     | |||                 | | ||| | |||   ||||||||||||||||| || ||||| || ||||||||||||||  | ||||| || ||  | ||||| ||||| ||||| |||||||| ||||
gttattttttttcatgtgttgatttctattatcttctgtgagtgggttcatgcatacctgatactactgacctttcacttttggattttcactagGATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAG

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------gtactcttactcttgagcaaagatt--ccctcttttctctggagcgttctgagttgcctattcttgtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG
                                        | |   |  |  |  |  | |||    |  ||  |  | ||   | | |          | || | |  ||  |||| ||||| ||||| || ||||| || |||| ||| ||||||||||| || |||||||  || ||||| |||||||| |||||||| ||||
gtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcacattgagtcatatttttacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG

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|58683649|gb|CK072336.1|CK072336
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|218504544|gb|FG949399.1|FG949399
EST:     CCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|218502457|gb|FG966789.1|FG966789
EST:     CACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|58598509|gb|CK009037.1|CK009037
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|12623249|gb|AU173462.1|AU173462
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG
EST: gi|58609933|gb|CK037966.1|CK037966
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATC
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATC
EST: gi|66914155|gb|CX101003.1|CX101003
EST:     TGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAANG                         GATGGGAT-ATGGAGCAATGGGAGAAATAAT-ACTACATCAGTGCCATAG
genomic: TGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAA-Ggtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAA-TAATTACTACATCAGTGCCATAG
EST: gi|5005377|gb|AU070539.1|AU070539
EST:     CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAANTGCCATAGC
genomic: CTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAG-TGCCATAGC
EST: gi|58609988|gb|CK038021.1|CK038021
EST:     GTTTATGAACTCTCACCAATATTTCTTCATAAG                         GATTGGATTATGGAGCAATGGGAGAATGATTACTACATCAGTGCCATAGCG
genomic: GTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCG

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: 61 (upstream exon), 66 (downstream exon)
Score: 71

CTCAGTGGCATCTTCAGCCAATCTTTGGGCCCTTATTATGGACGCGGGAACTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgtactcttac ... gtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagattccctcttttctctggagcgttctgagttgcctattcttgtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG
                                        ttcttgt  CT-rich tract
                                              tactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcttactcttgagcaaagattccctcttttctctggagcgttctgagttgcctattcttgtacttttagGATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG