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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTACCCAGAAACCCAGAGGATTTGGATTTATTACCTTTGCAGATCCTGCTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgtatgaatgtcggttaccagagtatgtcataagtttataagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcag

Basic information

species Oryza sativa
transcript LOC_Os08g23120.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23120.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G152526_T01 (Zea mays), 5'ss of exon 3
CTTTACCCAGAAACCCAGAGGATTTGGATTTATTACCTTTGCAGATCCTGCTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgtatgaatgtcgg---ttaccagagtatgtcataagtttataagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcag
||  || || || |||||||| ||||| |||||||| ||||| |||||  |||||||||||||||||||||||||  | |||||||| ||||||||   |||||| | |||| ||  |||   |   | |  |||||   ||  |     || | |  ||| |  ||     | || | |  || |  |||      |        |  | ||  |  ||    |  ||   | |    | |||                                                        
CTACACACAAAAGCCCAGAGGCTTTGGCTTTATTACTTTTGCTGATCCCACTGTTGTTGACAGAGTGATTGAGGATGAACATGTTATCAATGGAAAACCGgtaaactttttggttt-tgtctttggtttatatctttgtctcactctgtattagctcaatgtacatcatgtttcacgaaaacatatagtaaacaataagaagcgcttgtttgtgtagtttgaaatgtcatttactctaaaatgcag------------------------------------------------------

upper sequence: LOC_Os08g23120.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0015g00920.t01 (Vitis vinifera), 5'ss of exon 3
CTTTACCCAGAAACCCAGAGGATTTGGATTTATTACCTTTGCAGATCCTGCTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgtatgaatgtcggttaccagagtatgtcataagttta-taagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcag
 |  ||     | || || || ||||||||||||||||  || |||||| | ||||||||||| || ||||| || | |||||| |||||||||||| |||||||   | |  || | |||| ||  |   ||  | |  |||||  |  ||  ||  |      |   ||  ||       |||| |||||| || | || |||   |                                                                                         
GTACACGGGCCAGCCAAGGGGCTTTGGATTTATTACCTACGCTGATCCTTCAGTTGTTGACAGGGTTATTGAAGATACCCATGTCATTAATGGAAAGCAGgtaaaaaatatt-ttgcagttgttattttctttggtgttttccttgtaatttcctt-cactgtcttaaattgtca-------tcatcagtttagtatggtagtatttaa-----------------------------------------------------------------------------------------

upper sequence: LOC_Os08g23120.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv18s0117g00150.t01 (Vitis vinifera), 5'ss of exon 3
CTTTACCCAGAAACCCAGAGGATTTGGATTTATTACCTTTGCAGATCCTGCTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgtatgaatgtcggttaccagagtatgtcataagtttataagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcag
 | |||     ||||||| |||||||| ||| | |||| ||| |||||| | ||||||||||| || ||||| || |  ||||||||||| |||||  |||||||   | |  ||  | |   | | |||  |  |  | || |    |||| |||   |  |||  |      | |  | | | ||| | |||  | |   | |  |   ||                                                                                    
GTATACTGGTCAACCCAGGGGATTTGGGTTTGTCACCTATGCTGATCCTTCAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatct--tttttttcttttcttgatataataagctcat----gctttgtttggttgatgagga-----aaatcaagccttaaatatat--gctggaagaggaaggca------------------------------------------------------------------------------------

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|33656033|gb|CF278647.1|CF278647
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|572335|gb|D41846.1|D41846
EST:     CTGTTGTTGACAGAGTGATTNAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|1854338|gb|AA231854.1|AA231854
EST:     CTGTTGTTGACAGAGTGATTGAGGACA-CCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAAAACTAT
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTAT
EST: gi|58685113|gb|CK073800.1|CK073800
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|88393219|gb|CI616703.1|CI616703
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|38565648|gb|CK085101.1|CK085101
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|84117107|gb|CD150874.1|CD150874
EST:     CTGTTGTTGACAGAGTGATTGATGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|58680518|gb|CK069205.1|CK069205
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|88314669|gb|CI606737.1|CI606737
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|58686108|gb|CK074795.1|CK074795
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
EST: gi|88761436|gb|CI770992.1|CI770992
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCC
EST: gi|58664086|gb|CK052772.1|CK052772
EST:     CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAG                         GTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC
genomic: CTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTC

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: 75 (upstream exon), 68 (downstream exon)
Score: 25

CTTTACCCAGAAACCCAGAGGATTTGGATTTATTACCTTTGCAGATCCTGCTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtt ... aaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTCAAGACGAAGAAAATATTTGTTGGTGGATTACCATCTGCTTTGAAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTACCCAGAAACCCAGAGGATTTGGATTTATTACCTTTGCAGATCCTGCTGTTGTTGACAGAGTGATTGAGGACAACCATGTTATTAATGGAAAGGAGgtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgtatgaatgtcggttaccagagtatgtcataagtttataagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG