Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttatgctattagccccaaaatttaatattgaggcaatgctatatgatatataaaaaatattgccaaaaatctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT

Basic information

species Oryza sativa
transcript LOC_Os03g29260.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G37120.2 (Glycine max), 3'ss of exon 5
-----catttatgctattagccccaaaatttaatattgaggcaatgctatatgatatataaaaaatattgccaaaa-atctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT
       | | |  | | |      |  ||| |  || |  | |  |  |     || || |  |  |||  |    ||  |||     || || |  | ||| ||||||||||||||| |||||| | |||||||| ||||||||||| ||||| ||||||   |||||||| ||| | |||||   |||  ||||||| ||  |
gtgagtttctttcttgtcactagttatctttgaactttatcctaccccctcctccat-tataccactttgtgatggcattgattttctgctgattccct-tttcagCTGGGAAATCATCTGTTCTGTTGGATGTAAAACCATGGGATGATGAAACTGACATGAAGAAGCTTGAAGAATCAGTGAGATCTGTTCAGATGGAAGGGTT

upper sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
-----catttatgctattagccccaaaatttaatattgaggcaatgctatatgatatataaaaaatattgccaaaa-atctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT
       | | |  | | |      |  ||| |  || |  |  |||| |    |  ||| |  |  |||| |    ||  |||      | || |  | ||| ||||||||||||||| |||||| | ||||| || |||||||| || ||||| ||||||   ||||| || ||||| |||||   |||  ||||||| ||  |
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttc--tccatataccactttgcaatggcattgattctctgttgattccct-tttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
















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|88402149|gb|CI614992.1|CI614992
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAACAAAGAAT                         CTGGGACATCATCGG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGG
EST: gi|58682390|gb|CK071077.1|CK071077
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAACAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|33684663|gb|CF312902.1|CF312902
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|86510590|gb|CI153223.1|CI153223
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTATGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|86530287|gb|CI170493.1|CI170493
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|58606912|gb|CK034945.1|CK034945
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|25799116|gb|CA755077.1|CA755077
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGANATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAANCAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|87032513|gb|CI266153.1|CI266153
EST:     GGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: GGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|88213372|gb|CI213221.1|CI213221
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|427633|gb|D23766.1|D23766
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|86250485|gb|CI010146.1|CI010146
EST:     TCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: TCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|5851078|gb|AU078250.1|AU078250
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|88201644|gb|CI201999.1|CI201999
EST:     AGCAGAAGAACGGTCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|87035590|gb|CI190212.1|CI190212
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|88199311|gb|CI199161.1|CI199161
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|86592626|gb|CI253307.1|CI253307
EST:     GAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: GAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|87032231|gb|CI262013.1|CI262013
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|86512514|gb|CI155147.1|CI155147
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGACGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|33805318|gb|CF328537.1|CF328537
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|218480642|gb|FG944950.1|FG944950
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGACAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|89167249|gb|CI252780.1|CI252780
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|88830514|gb|CI010714.1|CI010714
EST:     GCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: GCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|88211491|gb|CI211131.1|CI211131
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|88970752|gb|CI385398.1|CI385398
EST:     AAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|87035579|gb|CI190201.1|CI190201
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|33813046|gb|CF332413.1|CF332413
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|89197781|gb|CI013771.1|CI013771
EST:     AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
genomic: AGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG
EST: gi|3768113|gb|AU032140.1|AU032140
EST:     GCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAAT                         CTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGANACAG
genomic: GCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAG

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: 73 (upstream exon), 74 (downstream exon)
Score: 67

GATGACGATGTTGATCTGTTTGGTGAGGAGACTGAAGAGGAGAAGAAAGCAGCAGAAGAACGGGCCGCAGCTGTCAAGGCTTCTGGAAAGAAGAAAGAATgtatgtattt ... tttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatatataaaaaatattgccaaaaatctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT
                                tactaac  putative branch site (score: 67)
                                      cttatcctttatttt  CT-rich tract
     atataaaaaatattgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttatgctattagccccaaaatttaatattgaggcaatgctatatgatatataaaaaatattgccaaaaatctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- -ttatgct
- - - - - - - - cccaaaa
- - - - - - - - - - - - - - - - - -gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccaaaa