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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

Basic information

species Oryza sativa
transcript LOC_Os05g03884.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggac-tctgtcttcca-attgatcttt--cacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
||||    ||    |  |||     |||| ||  |||  | | | | | |||   ||| |  |||||   |   |||   |       ||||| ||||| |||||||||||||| |||  |||||| || |||||||||||||||||||||||||||||||||||| ||||| ||||||||||||| || |
gtaaccatgcatgcat-cctggcaaacacgcagcagcagc-atcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG

upper sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G832409_T01 (Zea mays), 3'ss of exon 4
------------------------gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                        ||  |||  |  |     | |  |     || ||       | |    |  | | |    ||| | ||    ||   | ||   ||||| |||||||||||||||||||| || |||||||| || |||||||||||||||||||||||||||||||||||| ||||| |||| |||||||| ||||
gtaacatgctcacagcacacacctgtgctgtgactgatctttcctcgctttgaacgaacaatcgaatctgtgatcggcattttgctcagactaagtatct-tgttcggcagGAGGAGGATAAGGTGAGGCTGGCGGCCATGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCATTGGAAGCCGTCGG

upper sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaa---ttgatcttt-cacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
            |   || |     |   ||  |         | |     | ||   || |   ||||     | |||   ||   |||||  |   ||||||||| || ||  ||| |||  | | | | ||||| || |||| ||||||||| |||||||||||||| |||||||||||| |||| ||||| ||||| |
aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatt--tctggacacgtatctgaaaaggattgatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG

upper sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
-------------------------------------------------------gtaatgt-cgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                                                        || ||  || |  |  || || |     |       ||| |    | |  |   ||  |||  |  ||||   ||| |  |  ||||||  |  | |||  ||  || ||       || || || ||||| |||||||||||||||||||| || |||||| | ||| |||||||||| ||   ||
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttc--gttg-tgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
-------------------------------------------------------gtaatgt-cgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                                                        || ||  || |  |  || || |     |       ||| |      |  |   ||  |||  |  ||||    || |  |  ||||||  |  | |||  ||  || ||       || ||||| ||||| |||||||||||||||||||| || |||||| | ||| |||||||||| |||  ||
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttc--gctg-tgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

upper sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                               |        ||     || |||  |   | |||   ||    |||     |  |||||| |||| || |  |  || ||  |    ||||| ||||||| |||||| || ||||||||||| ||||||||||| ||| | || ||||| || || |
-----------------------------gtatgttgtgatagttttcattgaatttatattcttagtt--gtttggctggtttcagGAACAGGAGAAAGCTAACCTCGCAACTGATACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

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|88248839|gb|CI247923.1|CI247923
EST:     CTTACCCCACG                         GAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
genomic: CTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
EST: gi|86501605|gb|CI144238.1|CI144238
EST:     CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACG                         GAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
genomic: CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
EST: gi|66931257|gb|CX118105.1|CX118105
EST:     TGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACG                         GAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
genomic: CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
EST: gi|86489261|gb|CI131894.1|CI131894
EST:     CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACG                         GAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
genomic: CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
EST: gi|88956604|gb|CI092813.1|CI092813
EST:     CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACG                         GAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
genomic: CGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
EST: gi|86486530|gb|CI129163.1|CI129163
EST:     CTTACCCCACG                         GAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG
genomic: CTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAG

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: 35 (upstream exon), 57 (downstream exon)
Score: 3

CGAGTTCTTGAAGAAGAGGAAGAAAGGGAAACTACCGAAAGACGCGCGATCGGCACTTATGGACTGGTGGAACACACATTACCGTTGGCCTTACCCCACGgtaatgtcgc ... tctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                                             tctttcac  CT-rich tract
                                       aattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggactctgtcttccaattgatctttcacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG