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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGAAGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcggggtttcttcttccttcctcttcttgatttcgttcgccgccgattcgttggctgtggctcgtcgatgtcgatttggtggtggttcttggtt...

Basic information

species Oryza sativa
transcript LOC_Os06g12220.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G047860_T02 (Zea mays), 5'ss of exon 1
ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGAAGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcggggtttcttcttccttcctcttcttgatttcgttcgccgccgattcgttggctgtggctcgtcgatgtcgatttggtggtggttcttggtt---------
|   |  |  |            |  |     | ||||   | ||||||||| ||||||||||||||| |||||||||| |||||||| ||||| |||||||| |           || || |    || |  || |||||  | | | |||||| |||  | | ||   |  |      |   | |||| || ||   |         
AAAAGCAATAGTTCTGTTCTACTGGAGGAAGAGCAGGGAGCAAGATGGGGTCCGGATCTTTCCTCAAGGTGCTGGCCAATAACTTCGATGTCCTTGCCGGgtatga---------tttttttcccattccttctgttttcgcccacagacgattcattgattcttgcatatgtagcgttttcccgcggtgtttttttcctagggttcga

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G862101_T02 (Zea mays), 5'ss of exon 1
ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGA--AGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcggggtttcttcttccttcctcttcttgatttcgttcgccgccgattcgttggctgt-ggctcgtcgatgtcgatttggtggtggttcttggtt---------
    ||  |  ||    ||      || || |||  || |   | ||||||||| ||||||||||||||| |||||||||| |||||||| ||||| |||||||| |           || ||  ||| || | |||||||||  | |   |||||| |||| | | || ||  || | ||         ||  |  | || |         
--GAGGCCGATAGTTCTGTTCTACTGGAGGAGGAGCAGAGAGCAAGATGGGGTCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatga----------ttgtttgttcatccttttgatttcgcccccatgcgattcattggttctaggttcagcgttttctcgccatgtgttttcgtagggttcgacgtag

upper sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G177237_T01 (Zea mays), 5'ss of exon 1
ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGA--AGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcggggtttcttcttccttcctcttcttgatttcgttcgccgccgattcgttggctgt-ggctcgtcgatgtc----gatttggtg-gtggttcttggtt----
  ||  || |     |  ||     || || |||  || |   | ||||||||| ||||||||||||||| |||||||||| |||||||| ||||| |||||||| |           || ||  ||| || | |||||||||  | | | |||||| |||| | | || ||  || | ||    ||| || |  || |   | | |     
--CGCCGACGCCTCAACCTCATACTGGAGGAGGAGCAGAGAGCAAGATGGGGTCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatga----------ttgtttgttcatccttttgatttcgcccccaggcgattcattggttctaggttcagcgttttcccgcgatgtgttttgtagggttcgatgtaga

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|33662703|gb|CF293670.1|CF293670
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|33682572|gb|CF310811.1|CF310811
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|58600408|gb|CK010936.1|CK010936
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|58681131|gb|CK069818.1|CK069818
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|58690333|gb|CK079020.1|CK079020
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GGCATTAGTTTCACNTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCAC-TTGCTTATCCATT
EST: gi|88367310|gb|CI566276.1|CI566276
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|88760470|gb|CI770026.1|CI770026
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|117221019|gb|CT852619.1|CT852619
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|88745841|gb|CI769201.1|CI769201
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|3766943|gb|AU031053.1|AU031053
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCANTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|88431065|gb|CI574236.1|CI574236
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|2312240|gb|C28395.1|C28395
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|218478179|gb|FG968243.1|FG968243
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|86906935|gb|CI291277.1|CI291277
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT
EST: gi|426583|gb|D22408.1|D22408
EST:     TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGG                         GCCATTAGTTTCACTTGCTTATCCATT
genomic: TCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT

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: 54 (upstream exon), 73 (downstream exon)
Score: 36

ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGAAGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcgg ... acctttgcagGCCATTAGTTTCACTTGCTTATCCATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGAAGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcggggtttcttcttccttcctcttcttgatttcgttcgccgccgattcgttggctgtggctcgtcgatgtcgatttggtggtggttcttggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtgg