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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccttcaccagttctgtgttttgcatgtgttgacttaccgaaagcaaagaaacaatgcttgtctgcttgatgtcctgattctttatgtggaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTT

Basic information

species Oryza sativa
transcript LOC_Os05g01250.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092468_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------------gtccttcaccagttctgtgttttgcatgtgttgacttaccgaaagcaaagaaacaatg-----cttgtctgcttgatgtcc-tgattct-ttatgtggaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCT-AGATTCTGAGCTTAACTT
                                                            |  |    || |       ||||   |||    |  |      ||| | |||        || |||   || ||||| | ||| | ||   |||||||||||||||| |||||||||||||||||||||||||| |||||| | |||||||| || ||||| ||||||||  | ||| | || || || ||    |||  ||  
gtacggttcaactatcctgacactttgatttctcttggatatttgcaaacgctatatatatatatatatttttcaaaccgcatacattgctacaaagcttatgaaggagcaaaaactcctttatctctctgctgtccctcattttgtttcttggaaaatgcagAGCTCGATGCTTTGGAAGCCGACATGGACTTCGAATCAGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACC-

upper sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0073g00330.t01 (Vitis vinifera), 3'ss of exon 5
----gtccttcaccagttctgtgttttgcatgtgttgacttaccgaaagcaaagaaacaatgcttgtctgcttgatgtcctgattctttatgtggaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTC------AGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTT
     || |    |       |    || || |     ||     |  |   | ||| | |   | | ||  |  | |||| |    || ||     |||||||||||||||||||||||||  |||||||     ||     || |       || ||||| || || ||||| || |||||    ||| | ||  |||| ||      
gcacatcttgtttccaagaaataggctggatttagcagctgtttaattgggtaaaaaaatttggtatttgtatattttccttaacagttctgc----aatgcagAGCTTGATGCTTTGGAAGTGGACATGGGAACAGAGATGGATGCTGATGGGGTGCCCTCTTATCTCCAACCTGACAAGGACCATGATGTGGAAGCTGAACT------

upper sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0073g00340.t01 (Vitis vinifera), 3'ss of exon 2
----gtccttcaccagttctgtgttttgcatgtgttgacttaccgaaagcaaagaaacaatgcttgtctgcttgatgtcctgattctttatgtggaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTC------AGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTT
     || |    |       |    || || |     ||     |  |   | ||| |     | | ||  |  | |||| |    || ||     |||||||||||||||||||||||||  |||||||     ||     || |       || ||||| || || ||||| || |||||    ||| | ||  |||| ||      
gcacatcttgtttccaagaaataggctggatttagcagctgtttaattgggtaaaaaaatctggtatttgtatattttccttaacagttctgc----aatgcagAGCTTGATGCTTTGGAAGTGGACATGGGAACAGAGATGGATGCTGATGGGGTGCCCTCTTATCTCCAACCTGACAAGGACCATGATGTGGAAGCTGAACT------

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|55411056|gb|CV723432.1|CV723432
EST:     TGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: TGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|33655179|gb|CF277793.1|CF277793
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|33662788|gb|CF293755.1|CF293755
EST:     CGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: CGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|33655394|gb|CF278008.1|CF278008
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         G
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcag-
EST: gi|33655394|gb|CF278008.1|CF278008
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         G
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcag-
EST: gi|29687110|gb|CB683385.1|CB683385
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|27576216|gb|CA998910.1|CA998910
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|5003511|gb|AU068660.1|AU068660
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|88535886|gb|CI465601.1|CI465601
EST:     ACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: ACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|33689676|gb|CF317915.1|CF317915
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|5003512|gb|AU068661.1|AU068661
EST:     AAGAAGCTACAATGTNCCTGATGACATTGACGANGAAGAACNTATGGGGG                         AACTTGATGCNTTTGGAAGCCGACATGGACTTTTGAATCCAAATTTCAGT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGC-TTTGGAAGCCGACATGGACTTT-GAATC-AAATT-CAGT
EST: gi|27576887|gb|CA999581.1|CA999581
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|33655395|gb|CF278009.1|CF278009
EST:     TGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: TGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|117224782|gb|CT845909.1|CT845909
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|86870086|gb|CI318007.1|CI318007
EST:     AACTTAT-GGGG                         AGCTTGATGCTTT-GAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|88836570|gb|CI010826.1|CI010826
EST:     GAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: GAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|88834968|gb|CI370271.1|CI370271
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAAGTCCCC
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTC-AGTCCCC
EST: gi|218491828|gb|FG966677.1|FG966677
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAA
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAA
EST: gi|27577821|gb|CB000516.1|CB000516
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
EST: gi|88964831|gb|CI084829.1|CI084829
EST:     AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGG                         AGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT
genomic: AAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCT

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: 72 (upstream exon), 73 (downstream exon)
Score: 14

GAGATGATGGATCTTATGGATGTGAGCAATGAAATACAGGAAACTCTCGGAAGAAGCTACAATGTCCCTGATGACATTGACGAGGAAGAACTTATGGGGGgtatggatct ... gaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagaaacaatgcttgtctgcttgatgtcctgattctttatgtggaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTT
                            tcctgat  putative branch site (score: 14)
                                 attctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccttcaccagttctgtgttttgcatgtgttgacttaccgaaagcaaagaaacaatgcttgtctgcttgatgtcctgattctttatgtggaaaatgcagAGCTTGATGCTTTGGAAGCCGACATGGACTTTGAATCAAATTCAGTCCCCTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- ccttcac
- - - - - - - -tgtgttt
- - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - -accgaaa
- - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg