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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgatacgtactagtcctgtgttgaatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtacatatccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G079538_T01 (Zea mays), 3'ss of exon 10
---------------------------gtaacttgatacgt-actagtcctgtgtt--gaatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtacatatcca-----------ttttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC
                           || ||| |||   | |    || |||     |||    || | |       |  |    | |  |     || |||   |   ||||| ||  | |           ||| |||| |||||||| |||||||||||||||||||||| |||||||||||| |||||||||||||||||||||  |||||||||||| || ||||||||||| |
gtaccatattgcttacttgctactctggtgact-gatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAAGCAACTGAGGGGGCGC

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 11
gtaacttgatacgtactagtcctgtgttg---aatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtac-atatccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC
 || | | |  | || |   |||         ||  || | | || ||| |  || ||  ||     ||  |   |   | |||   ||   | |   |  |||| ||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||  ||||||||||||||| | ||||||||| |
-tatcctaaagc-tattgtacctagaaaagccaaaacacaaaacagcctatagtttggg-atggtgtatttactatgtatatcactgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaacttgatac-gtactagtcctg-tgttgaatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtacatatc-cattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC
     ||| | | | | |  |  ||   |||| |   || |||||  |  | ||  |  ||| |   |   |  |  || |  | |   |||   ||   |||||||||| || || || ||  |||||||||| || ||||||||||| ||||| ||||||   |||||||  || || |||||||||||||| ||  |  
---gtttgtttccgcaattcttttgacattgagtgataatatcatt-tgggcttttgagata-gttttgattgattcctcttctctgtgtattgtatcccagGGTCTTGTAGTTCCAGTCATAAGAGATGCTGACAAAATGAACTTTGCTGACATAGAGAAAACAATAAACGGTCTCGCTAAGAAGGCTACTGAAGGAACCA

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|86853753|gb|CI250004.1|CI250004
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|55436812|gb|CV731566.1|CV731566
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|88993275|gb|CI257703.1|CI257703
EST:     TATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GTTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|13421244|gb|AU175188.1|AU175188
EST:     TATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GTTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|88976995|gb|CI257691.1|CI257691
EST:     ACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: ACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|58613350|gb|CK041062.1|CK041062
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATGAGCATGAACTTTGCGGA
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGAT-AACATGAACTTTGCGGA
EST: gi|87021019|gb|CI271826.1|CI271826
EST:     ATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: ATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|25806798|gb|CA762759.1|CA762759
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGC
EST: gi|11233501|gb|AU164913.1|AU164913
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|5701685|gb|AU062775.2|AU062775
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTNATCCGAGATGCTGATAACATGAACTTTGCGGNC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|55435262|gb|CV730762.1|CV730762
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
EST: gi|58609985|gb|CK038018.1|CK038018
EST:     TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAG                         GGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC
genomic: TCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGAC

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), 71 (downstream exon)
Score: 68

AGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgat ... tccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgattgggttataagacatacatagtcactgtcatgtacatatccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC
 ctctgat  putative branch site (score: 68)
                                             tccatttt  putative PPT
           ttataaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttgatacgtactagtcctgtgttgaatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtacatatccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG