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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtactgcaccacatttattgcttttttatgagctcctccaatagaattactctggatccctggagcttaactaatacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC

Basic information

species Oryza sativa
transcript LOC_Os06g50300.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 15
--------gggtactgc-accacatttattgctttttta-tg-agctcctccaatagaattactctggatccctggagcttaactaatact--tttgttatcttttgtt---gcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
        |  | ||||      ||  | |    ||  | ||  |   ||  |||| |  |  |  | |   |    |||   ||  |  |  |||||| | |||||||   |||||| |||| |||||| |||||| | ||||||||| ||||||| ||||| |||||||||||||||| ||||||||||||||| ||||||||||| || || |
gtatatatgtatgctgctggtttatccactttcattacagtgtggggtctggaatacagct--tgagaagtaccaacgctgcgcttgttttgttttgttttgttttgtttttgcagGTCATCTTCTTCACCGACCCTATGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAGGAAGTTCCAGAACGTGTCCAAGGAGGGCCTGAAGC

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
-----gggtactgcaccacatttattgcttttttatgagctcctccaatagaattactctggatccctggagctta-actaatacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
        | ||||      |||||  |  ||  || |     ||  | |     | |   | |    |||  | |  ||    |||   || | | ||  ||||||| |||| |||||| ||||| || ||||||||| ||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||| || || |
gtattttatgctgctggtggtttatc-cacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
------------------------------gggtac-tgcaccacatttattgcttttttatgagctcctccaatagaattactctggatccctggagcttaa------ctaa---tacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
                                |||  |   |   |||  ||| | |||||  | |   |    |   |||   |||            ||||      ||||   || |||  ||    |||| | |||||||| | |||||| || || ||||| |||||||||||||||||||| ||||| || || |||||||||||||| || || |||||||||||| | ||||
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
-----------gggtactgcaccacatttatt-gcttttttatgagctcctccaatagaatta--ctctggatcc--ctggagcttaac----taatacttt-------tgttatcttttg------ttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
              |  |  |      ||||| ||| | ||||    | ||| || |  ||||  || |  || |  |||  |  | |     ||||   ||       | || ||||||        | |||||||| | |||||| || || ||||| || ||||||||||||||||| ||||| || || |||||||||||||| || || |||||||||||| | ||| 
ggtgcaatttaaattgtttgatttttattatttgctctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
gggtactgcaccacatttattgcttttttatgagctcctccaatagaattactctggatc-cctggagcttaactaatacttttgttatcttttgttgc-agGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
                          |||        | | ||||    | || |  ||   ||  | ||    ||| || ||      ||| |||| | |||| |||| |||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| ||||||||||| || |||||||| || || ||  
-------------------------gtttgcattgcacacgaataattcttctttaaatgatctccaactcgcataacacgttctcatacttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 13
--------------gggtactgcaccacatttattgcttttttatgag-ctcctccaatagaattactctgg----atccctggagcttaactaatacttttgtt-----atc-ttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
              |   ||| |      || |    |  || || || ||  ||  ||    || ||  ||    |||| |||   ||||| | |  |||| ||     ||| || | ||||||||||| | ||| |||||||| || || |||||| ||||||||||||| |||||||| || ||||| || |||||||| || || ||||| || || ||||
gtatgattggaaaagataactacttgcttttcaaccgtccttgattagtctggtcttattcttttcctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctattgcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATGGACTATGAAGACAAAAAATTCCAGAATGTGTCAAAGGAAGGCCTGAAAC

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|58693264|gb|CK081951.1|CK081951
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
EST: gi|87016979|gb|CI286115.1|CI286115
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
EST: gi|58684599|gb|CK073286.1|CK073286
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
EST: gi|32947850|gb|BP184422.1|BP184422
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
EST: gi|32947910|gb|BP184482.1|BP184482
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTTACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
EST: gi|29627895|gb|CB632906.1|CB632906
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
EST: gi|29659228|gb|CB655503.1|CB655503
EST:     AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAG                         GTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG
genomic: AATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATG

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: 74 (upstream exon), 73 (downstream exon)
Score: 46

GAAGCCAGGGCAGAAGGACATCTTTTACATTACCGGAAGCAGCAAGGAACAATTAGAGAAATCACCGTTCCTTGAGAGGCTAACCAAAAAGAACTACGAGgtgtgttacc ... tttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattactctggatccctggagcttaactaatacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC
                         aactaat  putative branch site (score: 46)
                                 cttttgttatctttt  CT-rich tract
                       ttaactaatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtactgcaccacatttattgcttttttatgagctcctccaatagaattactctggatccctggagcttaactaatacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- -tactgca
- - - - - - - - - - tgctttt
- - - - - - - - - - - - - - - - - ctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctgga