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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagccttcgtagttgtagtccttaggaaattttgtgcagcctaaaatggtcatccgttgtagacaaatcctgattgttttctgtttttcatttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG

Basic information

species Oryza sativa
transcript LOC_Os02g57854.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G26580.1 (Glycine max), 3'ss of exon 4
-gcaagccttcgt-agttgtagtccttaggaaattttgtgcagcctaaaatggtcatccgttgtagacaaatcct--gattgttttctgtttttcatttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG
  |  |   || |  ||| |   |||   |  |  |    |  ||    ||    |   ||| |  ||||||     |||  |   || ||||||| |   |||||||| || |||||||||||  |||| ||||| || |||| |||||||||||| ||| | || ||||| || || |||||||| ||||| || ||||| |
gacttgtgatctttggttatgaccct---gctacctcccacc-cccggtatccctacatgttttccacaaattgaaagatcttacactttttttcactgtgcagGTTGCAAATATGATAAGGTTTTTGGTTGATAGTTATAACAAGCCCGTTCCTGCAATACTTGAAATCCCTTCTAAAGATCATCCTTATGATCCGGCACATG

upper sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 4
-gcaagccttcgtagttgtagtccttaggaaattttgtgcagcctaaaatggtcatccgttgtagacaaatcct--gattgttttctgtttttcatttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG
  |  |   || | | |  || || |   |            ||    ||    |   ||| |  | |||| |   |||  | | || |  |||  |   |||||||| || |||||||||||  |||| |||||||| |||| ||| |||||||| ||| | || ||||| || || || ||||| ||||| |||||||| |
tacttgtgatcttgggttaagaccctgctacccccaac---tcccggtatcccgacatgttttccataaattcaaagatcttatactttccttcgctgtgcagGTTGCAAATATGATAAGGTTTTTGGTTGATAGCTATAACAAGCCTGTTCCTGCAATACTTGAAATCCCTTCTAAAGACCATCCTTATGATCCAGCACATG

upper sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 4
gcaagccttcgtagttgtagtccttaggaaattttgtgcagcctaaaatggtcatccgttgtagacaaatcctgattgttttctgtt--tttcat-ttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG
   |       |||    || |||      || |  |  |  ||  || |    |   ||      |  ||   | |||  |  |    ||||||  |   || | || || |||||  ||||| |||||||||||||||||| ||| |||||||| || ||||||||||| |||||||| ||||| ||||| || || || |
---acatgaaatagaatgaggcctatctctatgtgctctatactgcaaagtctgtttctttctacaatgtcaaaaatgtaatgagaaagtttcatgcttgtagATCGCCAATATGATCCGGTTCTTGGTGGATAGCTACAACAAGCCAGTTCCTGCAATCTTGGAGATCCCTTCCAAGGACCATCCCTATGATCCTGCTCATG

upper sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 4
gcaagccttcgtagttgtagtccttaggaaattttgtgcagcctaaaatggtcatccgttgtagacaaatcctgattgttttctgttttt----catttga----cagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG
      | || |      |      | |||||||  ||  |       | |  ||  |  |||   | |  || ||| | |    |  |     ||| |||    |||||||||||||||||||||||||| || ||||||||||||| ||| || || || ||  ||||||| ||||||||||| ||||| || || || || || |
------catcttgacaaaataaaaaatgaaatttcatgagggtggcctttgatatttg--gtatgaagagtctaattatgtgtaatcatcatggcatctgaatttcagGTTGCGAACATGATAAGGTTCCTAGTAGATAGCTACAACAAGCCGGTACCAGCAATTCTGGAGATTCCATCCAAGGACCATCCTTACGATCCTGCTCATG

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|55433570|gb|CV729893.1|CV729893
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88242157|gb|CI242006.1|CI242006
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGTTAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88477930|gb|CI415201.1|CI415201
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88353826|gb|CI634617.1|CI634617
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88334071|gb|CI641122.1|CI641122
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCG
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCG
EST: gi|86523723|gb|CI163929.1|CI163929
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|112785856|gb|EE591550.1|EE591550
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCACCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88363322|gb|CI643180.1|CI643180
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88310002|gb|CI657426.1|CI657426
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88490588|gb|CI427860.1|CI427860
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88505127|gb|CI432633.1|CI432633
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88339191|gb|CI633762.1|CI633762
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88242883|gb|CI240734.1|CI240734
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88216147|gb|CI215996.1|CI215996
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|55433572|gb|CV729894.1|CV729894
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88979436|gb|CI025938.1|CI025938
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88475489|gb|CI412760.1|CI412760
EST:     CAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: CAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|86910935|gb|CI294835.1|CI294835
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTG
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTG
EST: gi|86529211|gb|CI169417.1|CI169417
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|3761016|gb|C98270.1|C98270
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|86593735|gb|CI266415.1|CI266415
EST:     AATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88333055|gb|CI640898.1|CI640898
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTG
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTG
EST: gi|88261929|gb|CI365505.1|CI365505
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTCCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
EST: gi|88282577|gb|CI403973.1|CI403973
EST:     AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATAT                         GTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT
genomic: AGGAATTCACTACAAGGGAGGACATTGCAATTGTTCTCATCAGCCAATATgtaagtatct ... catttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggtcatccgttgtagacaaatcctgattgttttctgtttttcatttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG
                        tcctgat  putative branch site (score: 3)
                                 ttttctgtttttcatt  putative PPT
                                        tttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagccttcgtagttgtagtccttaggaaattttgtgcagcctaaaatggtcatccgttgtagacaaatcctgattgttttctgtttttcatttgacagGTTGCGAACATGATAAGGTTCCTGGTGGATAGCTACAACAGGCCCGTTCCTGCTATATTGGAGATCCCATCCAAGGATCATCCGTATGACCCAGCACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC