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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG

Basic information

species Oryza sativa
transcript LOC_Os08g10410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 3
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtg--tgaagaacgttccgcctgcatctctgccctatacgttatccgattgtaca---aacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
|||||  ||| |||| |      ||  | |  |||| |||    |    |||| |  || ||   |||   |  ||   | |  | |   | |  |  | ||| | ||| ||  |||  ||    | ||| |  ||| ||||  || ||  || || |||||||||| ||||||||||| |||||||| ||||| ||||| || ||||| || ||||||||||||||||||
gtaatataagccacatacctgcattgtattattcttgcttcctttcttgagtt-tcaaggttatatgttgttttagtcagatgtgtcaagagcagttacatatgcattagccagttgatcacttgatctacgtgtctaaaattgtg-tctattgtctatcagGATCGTATTATTGCTCGGCTGCAACAGCCTTATTCCCTTGACTGCATACCAGTTGAAGCTGAATACCAG

upper sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 3
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
                                   || |   | ||| ||||  ||  |   | || |||||   | | |    ||  |   ||    | | | || |  |||| |   ||         |  ||||  ||             |||||||||||||| ||||| || || || || || ||||| |||||||||||||||||||| ||||| |||
---------------------------------tcttttcctgcttaacagtagttggg---gcttatgtgatcca-gatataactagacaactattatgtgctttctgagattatttcaatg-------ccaaaattttg-------------cagGATCGCATTATAGCTCGCCTACAGCAGCCATATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG

upper sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
                                   || |   | ||| ||||  ||  |   | |  |||||       |||   |  | ||   |    ||   | | |  |   |||    |  |   |  ||||                 |||||||||||||| ||||| || || || || || ||||| |||||||||||||||||||| ||||| |||
----------------------------------cttttcctgcttaacagtagttggg---gctcatgtga-------tccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaat-------------ttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG

upper sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttt-tccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
                                              |  ||   ||| || |    || | ||||     | ||||     | |   | ||  || | ||  | ||  ||   |||     |  |  | |  ||  ||| |  | ||||||||||| |||||||| || ||||||||||| || || ||||||||||| |||||||| ||||| |||
--------------------------------------------acattagc--ttctgagta--cgtcttaaga-----ctgccttatcttttagtcaatttgtgaccctctagttgaagtttat-----tacatcatttgtctgtttatataacagGATCGCATCATTGCTCGTCTCCAACAACCTTATTCGCTAGATTGCATTCCAGTTGAAGCAGAATATCAG

upper sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 3
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaa-cctatgcatctgaaataatg--atcctttttccat-----cagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
                                                                ||   | |   || | |  | |||||||    |  | | || |   ||    |  || ||| || | |  | ||   |  ||| || ||||||     |||||||||||||| ||||| || |||||||| || || || ||||||||||| || ||||| ||||  |||
----------------------------------------------------------------tttcttcatatacatac-acatgcatcttcagcacacaggtaaaatgacatcattaatcctgtgtaacatatatgcgggaatctttgttccattttggcagGATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG

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|88315515|gb|CI615387.1|CI615387
EST:     AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAG                         GATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCT
genomic: AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAGgtaattgaag ... tttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCT
EST: gi|88336875|gb|CI626955.1|CI626955
EST:     AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAG                         GATCGCATTAT
genomic: AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAGgtaattgaag ... tttccatcagGATCGCATTAT
EST: gi|218479983|gb|FG957518.1|FG957518
EST:     AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAG                         GATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCT
genomic: AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAGgtaattgaag ... tttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCT
EST: gi|88372600|gb|CI610923.1|CI610923
EST:     AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAG                         GATCGCATTATTGCTCGACTGCAACAA
genomic: AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAGgtaattgaag ... tttccatcagGATCGCATTATTGCTCGACTGCAACAA
EST: gi|88313765|gb|CI597396.1|CI597396
EST:     AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATT-AAAACAAG                         GATCGCATTATTGCTCGACTGGAACAACCTTACTCCCTCGATTGGATTCCT
genomic: AATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAGgtaattgaag ... tttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCT

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), 51 (downstream exon)
Score: 18

TAAAAATATTGCTCATCTGACTCACGTTAGTGAGATGGAGAAGAAGTGTGAATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAAACAAGgtaattgaag ... tttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
                                        tcctttttccatc  CT-rich tract
                               aaataatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA