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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag

Basic information

species Oryza sativa
transcript LOC_Os06g07630.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G173849_T01 (Zea mays), 5'ss of exon 2
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag
||||||| || |||||||| || |||||||| || ||||||||||| || || || || ||||||||||| |||||||| || || ||  | ||||| |||||||  |   | |    ||||||| | | || |             || ||| | | ||    |    | |  | | ||||  ||| |  || || |   |    |  |||||                       
CAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATCGGCACCAAACGTTTTGATAGgtatgcct--tttatgacatttttagctcttgca-------------tggttctattcctgctttg-gctgatgatactctttatgagatgaaaatgtgaatcagttgcacaagac---------------------

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 6
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtat-gtctcacatgatttttatcccctggaattt-ttcctacattgtttca-aattctata-atataatcaaaacatt-----cttattgaaaaaaata-tattcttattgttaacaagcattttgctttattctatgacag----------------------------------------------------
||||||| || |||||||| || |||||||| || ||||||||||| || || || || ||||||||||| ||||||||||| || ||  | ||||| |||||||| | || | ||||  |   |     |  || ||| |||||   |||  | |  || || |  |||  || ||||  ||     | |||  |  |  | |  | | || |||||   |   | | |     | ||  |   |                                                     
CAAAGCTTGTCCGGGATGCATTCCAGCTTGCCAAAGAGAAAGCTCCTTGTATTATATTTATTGATGAGATAGATGCCATTGGCACCAAACGTTTTGATAGgtatgttttgtatgacattttcagttcatgcatgattttattcctgttttggctgatgatactctttataggatgaaaatgttaatcgcctatacaggatcagagcactttttttgtttcaatttagtgtaaacaaatcattcttattaggaagaagcttatctgatgcatgctccataattttgttctcttggtacag

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag
||||||| || || ||||| ||||| ||||| || ||||||||||| ||||| || ||||| ||||| || ||||||||||| || ||| | || ||||||||   || | |  | |||||   || |     |  | || || || | | |||   | | |  |  |||||   ||||||| | |   | | || |                                        
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttc-tgattccaattc-----atgtatttctgcactttctcag-ctatttgctcaaatca---cattctt-tggttgagagtacag---------------------------------------

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 6
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcct-acattgtt-tcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag
| || || || || ||||| |||||||||||||| |||||| |||| ||||||||||| || ||||| ||||||||||| || || ||| ||||||| |||||           ||| |||  | |  |     || |||| | | ||| || ||||| |  ||  |  | | |||  ||     |  |   |     |  ||  |||   | |  |  ||| ||   || |||  |||
CGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAGGCACAAAGCGGTTTGATAGgtaaac--------cattattggtttagcactacatctttcatgatatttttatcaaaatggatt-tggattgaaattatcaaggtgaactcatgagcagcctccttgactatagac--ttttctgccttttattgcag

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 5'ss of exon 7
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattc--tataatataatcaa--aacattcttattgaaaaaaatatattc--ttattgttaacaagcattttgctttattctatgacag
|||| || ||||| ||||| || |||||||| || |||||| | || || ||||||||||||||||| |||||||||||||| || ||| | ||||| |||||| |  || |   ||  |    ||    ||   | ||| | |  |||    | || |  ||   || || |||     | |  | || |  ||||  | |||  | ||||||   |      |||  ||||| ||  ||||
CAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTGGCACGAAGCGTTTTGATAGgtatct-cgtgttctatcttgcaaattagttgc--tctttacaaatttgacggagatgcattacggtacaaccaatggggagtgctgtttattaaaaagtgttcagtgattgttgtta------ttgtgttattttactacag

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EDP05634 (Chlamydomonas reinhardtii), 5'ss of exon 2
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACA--Ggtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag
                         ||| || ||||||||  | ||||||||||| ||||||||||||||||| ||||| || || ||| | || |||   |   |||  |     |  ||  |     |  ||| |  ||     ||   ||   ||   | |  || ||     |||  ||       |   | | || | | |        |||    |||   |           
----------------------CGCGCTGGCCAAGGAGAAGTCGCCCTGCATCATCTTCATTGATGAGATTGACGCCATCGGCACCAAGCGCTTCGACTCCGAGCTGTCGGGAGACCGCGAGgtgggagctttgggaggttcggcgcaggattgggaaacgtgtgttacaa---ggacagactcgc---gacgcacacatgcgtgtaccgggtgagcgcgctgcgcca-----------

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 6
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatat---attcttattgttaacaagcattttgctttattctatgacag
|||| || ||  |||| || || ||||| || ||||| ||||||||||| ||||| |||||||||||  | ||||| ||||| |||||| | |||||||||| ||||    || | | |   |         |||  | |  || |  ||||  |     |   || | | |      ||  |||||  | | |||   | |||||||  | ||  |   || | |||||    || |||
CAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTGGTACTAAGCGTTTTGACAGgtttgtaatgttctcttcaaagtgtctatacagaacatcttgtagagcgtttttagaggaagggtacacttatcttggtcaaattgattatattatgacaatcttatttgtgacttgatcttcggtttatgt--tggcag

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ37626 (Selaginella moellendorffii), 5'ss of exon 6
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag
||||||| ||  | ||||| |||||||| || || ||||| || ||||||||||||||||| |||||  | || || |||||||| ||  | ||||| |||| ||   |||||| |  |     |   || |    ||| |  ||| ||  | | || |                                                                              
CAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTGGGACCAAACGTTTTGATAGgtttg---gtctcaaa--acggacacggccgg----tttactaacagtgacttacatacag----------------------------------------------------------------------------

upper sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ15061 (Selaginella moellendorffii), 5'ss of exon 6
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag
||||||| ||  | ||||| |||||||| || || ||||| || ||||||||||||||||| |||||  | || || |||||||| ||  | ||||| |||| ||   |||||| |  |     | |  | ||   ||| |  ||| ||  | | || |                                                                              
CAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTGGGACCAAACGTTTTGATAGgtttg---gtctcaaa--acggacaccggccgg---tttactaacagtgacttacatacag----------------------------------------------------------------------------

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|27577580|gb|CB000275.1|CB000275
EST:     ATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAG                         TGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
genomic: ATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgt ... tctatgacagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
EST: gi|88326087|gb|CI651141.1|CI651141
EST:     ATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAG                         TGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
genomic: ATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgt ... tctatgacagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
EST: gi|2427528|gb|C71991.1|C71991
EST:     ATCATTTTNATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAG                         TNAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
genomic: ATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgt ... tctatgacagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
EST: gi|86435620|gb|CI106853.1|CI106853
EST:     TAAGAGCTTTGACAG                         TGAGTTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
genomic: TAAGAGGTTTGACAGgtatgtatgt ... tctatgacagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
EST: gi|163918277|gb|EG713191.1|EG713191
EST:     ATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAG                         TGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA
genomic: ATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgt ... tctatgacagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAA

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), 70 (downstream exon)
Score: 45

CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgt ... tctatgacagTGAGGTTAGTGGTGACAGAGAAGTTCAGAGGACTATGTTGGAATTGCTGAACCAACTCGATGGATTTAGTAGTGACGAGCGGATAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCTGGTTCGGGATGCTTTTCAGCTTGCTAAGGAGAAAGCTCCCTGCATCATTTTCATTGATGAGATTGATGCCATTGGGACTAAGAGGTTTGACAGgtatgtatgtctcacatgatttttatcccctggaatttttcctacattgtttcaaattctataatataatcaaaacattcttattgaaaaaaatatattcttattgttaacaagcattttgctttattctatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG