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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g57140.2
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 21
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaatttctattgct---ccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcag
|||| |||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||| |||||||||||||||| || || ||||||| | ||   |  ||    |  | |||      |||||  || |||   | ||    || | || |  |   || ||||     |||   ||| |   ||       
TGCTTATGAGTGATTCTCTGGGAGGGAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCAGAGTCTAACTTGGAGGAGACTTACAACTCGCTGATgtatgtactttggtcactgagtctatgtaccctgtcttttggatt-tgctttttgtcactgtttccatcaatgtggtcttgat--atattagcttttccatat-------

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 21
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaatttctat-tgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtat-tgactggcattttttttcctccatcttgcag
|||| |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||| ||| |||||||||||||||| || || |||||||   |||| | | | |        | ||    | || |  ||    || |  | ||  ||   |      ||| ||  |   || | ||  | | |         
TGCTTATGAGTGATTCTCTCGGAGGCAATGCGAAGACCTTGATGTTTGTGAATGTTTCACCAGCTGAGTCTAACTTGGAGGAGACTTACAACTCGCTAATgtatgtgcttctttgttcactgagtcttatgttccctcgtctcttggatttgctatttgt-cactgtttccatctatgtggttttgatatattagctttcc--------

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 23
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcct--ccatcttgcag------------------------
|| ||||||||||||| ||||| || ||||| |||||| | |||||||||||||| || |||| ||| || | | |||| || ||  | || || || |||||||  |||||  | ||    |     |    |     |||   |  |     ||  |  | |  | ||   | ||| || | || | || || |     |||   |                         
TGTTGATGAGTGATTCACTTGGGGGTAATGCCAAAACCCTCATGTTTGTGAATGTATCTCCAGTAGAATCAAGCTTGGATGAAACACATAACTCTCTAATgtatgtttttcttatccttgttttcttgaactctacaaagtt-cacttccaaatctttta-atagttttttttttttggctagtatgtattctcttagtgttctaataatctttatattttatgctaattcag

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 22
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 5'ss of exon 24
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt--ctattgctccagta-tacaagtctttttgtgttatgcc-cctggtgctcgtgtacac-ctgttgagtattgactggcattttttttcctccatcttgcag---------------------------------------------
|||| ||||| |||||||| || || |||||||| ||| | |||||||| ||| |||||||||||||||| || ||||| |||||  | |||||||||  ||  | |     ||||| ||  |||  |   |||    |  |   || |    || || |  |  | || |    |||    ||  ||  |||    || |   |  |                                                 
TGCTTATGAGCGATTCTCTCGGTGGAAATGCGAAGACCCTCATGTTTGTAAATATCTCACCAGCAGAGTCTAATCTGGACGAGACCCATAATTCACTCTGgtgaggaacggactatttcttgagtcctgtcagttcactactaaaattcaatttgatgtttctcgatactccagagaggtaagaagggggtttccagtcattagtgataagtacgtagtgatttttttgattgacctttattgttggtgtattgtag

upper sequence: LOC_Os04g57140.2 (Oryza sativa), 5'ss of exon 22
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 23
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatg-aatttctattgctccagta----tacaagtctt---------tttgtgttatgcccctggtgctcgtgtacacctgttgagtatt---gactggcattttttttcctccatcttgcag----------------------------------------------------
|||| ||||| ||||||||||| || |||||||| ||  | |||||||| ||| ||||||| ||||||||||||||||| |||||  | |||||||||  ||  | || |  | | ||||  ||     | ||| | ||         |||    |   |   || ||    |  |  |   |  ||  |    ||  |  |||| |     |     |||                                                       
TGCTCATGAGCGATTCTCTTGGTGGAAATGCGAAGACACTCATGTTTGTAAATATCTCACCGGCAGAGTCCAACCTGGATGAGACCCATAATTCACTCTGgtgagtaactgatctggctcgtgttcctttccaatttttatctttattttttcacttcacttttgatgtctctagattctaataaaggttcaaagatggagatttctagatgtatgagttgatttgatttccagcctgaaaatgcttacttctgacttctgttgttgtattggtag

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|88688275|gb|CI731851.1|CI731851
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88690249|gb|CI734328.1|CI734328
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88691367|gb|CI733950.1|CI733950
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|218496230|gb|FG959153.1|FG959153
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTATCACTGATACGAGCAAGCATGTAGA
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88966705|gb|CI365928.1|CI365928
EST:     ACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGGTCAATGATACGACCAAGCATGTTG
genomic: ACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATT-GTCAATGATACGAGCAAGCATGTTG
EST: gi|88691416|gb|CI733494.1|CI733494
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88688222|gb|CI731798.1|CI731798
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88690034|gb|CI734113.1|CI734113
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88691225|gb|CI735304.1|CI735304
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88688756|gb|CI732332.1|CI732332
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTCGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
EST: gi|88690953|gb|CI735032.1|CI735032
EST:     AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCAT                         GTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC
genomic: AATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGC

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: 16 (upstream exon), 60 (downstream exon)
Score: 1

TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaattt ... catcttgcagGTATGCTTCACGAGTGCGTTGCATTGTCAATGATACGAGCAAGCATGTTGCCCCAAAGGAAATCATGAGGTTGAAGAAGTTAATTGCTTATTGGAAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGATGAGTGATTCTCTTGGAGGCAATGCGAAAACCTTGATGTTTGTGAATGTCTCACCAGCAGAGTCCAACCTGGAGGAGACTTACAATTCACTCATgtatgaatttctattgctccagtatacaagtctttttgtgttatgcccctggtgctcgtgtacacctgttgagtattgactggcattttttttcctccatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA