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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgttttttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 25
----------------gtatagtttctta--ttgacttcttgttttgttgtga-gctaggactgttatatcaagtaatgttttttgtatccatcttatc-gtaatgatttt-ttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
                 |    | |||||  |       |||  |  |  | |   ||  || |  ||  ||  |    | | |  ||||||||      || | |||||  || || |||||||||| || ||||| |||||||| |||||||||||||| |||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||  
gtattgtctcagttttttgagctctcttaactgagggagttgcctcataattataataaaaccgacattacagttgcattatatcttatccatccaggaagtgacgatttcctttctttgcagCAAGAGTTAATCAGGACAGTTGATCTTGGGCCTTTCAAACATGTTGTAGATGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACTTTAT

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 25
-------------------------------------------------------------------------------------gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgttttttgtatccatcttatcgtaatgattttttc-----ctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
                                                                                      | ||      | || | ||  |  | | || ||   |||     ||     || ||     | ||||||   |      | | | |||||         |   ||||||||  | || || |||||||| ||||| |||||||||||| ||||||| ||||| |||||| | ||||| || || ||||||||||| || ||||| |
gtaatctgaattgtgccattctgttccatgtatttcagttgagtatatagcattacaataaaacttgactttatactccccattattctaagaatattttaatttagtaatatattttgcaatagctgcatttaccaaaatagaagatcttgtattactggaggtggactcattttaatgaaattttgacagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTAC

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 26
gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgtttt----ttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
  ||| ||| | || |  || |  | |  | |  || |     |   | |  |    || || |     || |    ||| ||  ||||||  ||||      ||||||||  | || || |||||||| ||||| ||||| |||||| ||||||| ||||| |||||| | ||||| || || ||||||||||| || |||||||
--atactttgtaatggctttttaatctactagaaagatgcctttaacaaaatagaagatcttgtattactggaggtgtctcattttaatgaaattttg----acagCAAGAGCTCATAAGGACAGTTGATCTTGGTCCTTTTAAGCATATTGTGGATGATGGACTTGAATTGAGGAAGGCGGCTTTTGAATGTGTAGACACATTGC

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 25
gtatagtttcttattgacttcttgttttgttgtgagctaggac-tgttatatcaagtaatgttttttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
||| ||||  | | ||| |    |    ||||| | ||  | | | | |||      || ||||| | | ||||||    | | |    ||| || | ||||| ||||||| ||||| || ||||| ||||| || ||||||||||||||||| || || || || || |||||||| || ||||| ||||||  |||  || 
gta-agttcttcagtgattca--gcacagttgttatctgtgtcatataatacattagaaggttttatct-tccatc---gcctgagacatttatcttttgcagAAAGAATTAATCAGGACGGTTGATCTTGGTCCATTCAAGCATGTTGTGGATGACGGGCTCGAGCTGAGGAAAGCAGCTTTTGAGTGTGTGTTTACTCTGG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 26
gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgttttttgtatccatcttatcgtaatgatt--ttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
 | |  |     ||| | |  || | |  || |    |    || || | |  | | ||      ||    |   | |   |  || ||  | || || |||||||||| || || |||||||| || ||||| |||||||||||| ||||||| ||||||||||| || |||||||| || ||||||||||| || ||| |||
-tctgctactaaatttattgtttttatccttttccttttttgctattctttttattgataccaagtga---cggttaaatattctgtttcatgtttctatgcagCAAGAGTTAATTAGAACAGTCGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGTCTTGAGCTGAGGAAAGCAGCTTTTGAATGTGTAGACACACTGC

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S35_209V6.1 (Physcomitrella patens), 3'ss of exon 25
gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgttttttgtat-ccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
 | |  | | || || ||| |  || |   | |     || ||    || |   |||       ||||   | |  ||||  | ||  ||  |   |||| || ||||  | ||||| || || || ||||| |||||||||||| ||||||| ||||| || ||||||||||| |  |||||||||||||||||||| ||||
-tcttctgttttgtttactccgcgtctgccttttgttcagaacaacgatctgtggtatccgcagttgttcactaaattat--tcatcgttggtggatgtgtagAAAGAGCTCATCAGGACCGTGGATCTTGGTCCTTTCAAGCATATTGTGGATGATGGGCTGGAACTCAGGAAGGGAGCCTTTGAATGTGTGGATACCTTGC

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S337_6V6.1 (Physcomitrella patens), 3'ss of exon 24
gtatagtttcttattgacttct-tgttttgttgtgagctaggactgttatatcaagtaatgttttttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
   |   ||||   |||||  | |||  |  | |  | ||   |    |  |||   |  | | |   |  |||   | |  |||   |   ||  | || || ||||  | |||||||| || || ||||| |||||||||||| ||||||| ||||| || |||||||| || |  || ||||||||||||||||| ||||
---tttattctctatgactggtatgtgctaatcttggttattgccaggagttcactaatcgctctggcttgccaatatgtgttaaacgtgggttggtttgtagAAAGAGCTCATCAGAACCGTGGATCTTGGACCTTTCAAGCATATTGTGGATGATGGACTAGAACTCAGAAAGGGGGCTTTTGAATGTGTGGATACCTTGC

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|58654892|gb|CK043572.1|CK043572
EST:     GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAG                         CAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
genomic: GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
EST: gi|38473429|gb|CF957561.1|CF957561
EST:     GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAG                         CAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
genomic: GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
EST: gi|66914920|gb|CX101768.1|CX101768
EST:     GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAG                         CAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
genomic: GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
EST: gi|32948231|gb|BP184803.1|BP184803
EST:     GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAG                         CAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
genomic: GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
EST: gi|58667112|gb|CK055798.1|CK055798
EST:     GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAG                         CAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
genomic: GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
EST: gi|29625622|gb|CB630633.1|CB630633
EST:     GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAG                         CAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC
genomic: GTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGAC

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: 69 (upstream exon), 68 (downstream exon)
Score: 27

TGTGCTGGCCTTGAGTACAGCTGCCCACAACAAGCCAAATTTGATTAAGGGTCTTCTTCCTGAATTATTGCCTCTTTTGTATGACCAAACTGTTGTTAAGgtatagtttc ... tcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcaagtaatgttttttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC
                                        ttttttcctgt  CT-rich tract
        taatgttttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtttcttattgacttcttgttttgttgtgagctaggactgttatatcaagtaatgttttttgtatccatcttatcgtaatgattttttcctgtgcagCAAGAATTGATCAGAACAGTTGACCTTGGGCCTTTCAAGCATGTTGTGGACGATGGTCTTGAACTCAGGAAAGCTGCCTTTGAATGTGTGGATACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC