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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttatctattttttttctatatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG

Basic information

species Oryza sativa
transcript LOC_Os11g01439.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01439.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 5
-----------------------------gtaagcttatctattttttttctatatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG
                              ||    | ||      |      |||   ||  |||||| |     ||||||| ||| ||| ||||  || ||||||||| |||||| | ||||| ||||| || ||||||||||||||||||||||| |||||| ||||||| ||||| |||||||| || || ||| ||||  || 
gtaagcagcccgaacatgcccttcatacaatacctctgtcatgaagtagcaattattgtacttatgacacatgttctagtact-aaagaggatcaa-caaaattttagGTTGATGAGAGAGCAGTGCTAAAACATTTTGATTGGCCAGAGAGCAAAACAGATGCAATAAGAGAAGCAGCTTTTGAGTACCAGGATCTGATAAAGCTAC

upper sequence: LOC_Os11g01439.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 2
gtaagcttatctattttttttctatatgcaacac----atgacaaaatagttagtactgaaaaagggtcaaata---acattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG
||||||    |          ||  || | ||||     | ||||| ||     || || |     | || ||    ||||||||||| |||||||| |||||  ||||||| ||||||||||||||||||||||| |||||| ||||||| ||||| ||||| || || || ||| |||| ||| 
gtaagca-gcccgaacaggccctccatactacacctttgttacaaagtaccagttattgtacttatgacacattttcacattttagGTTGATGAGCGAGCAGTGTTAAAGCATTTTGATTGGCCAGAGAGCAAAACAGATGCAATAAGAGAAGCAGCTTTTGAATACCAGGATCTGATAAAGTTAC

upper sequence: LOC_Os11g01439.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g02860.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gtaagct---tatctattttttttctatatgcaacacatgacaaaatagt-tagtactgaaaaag-ggtca------------------aataacatttt-------agGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG
                        ||| ||   |||   ||| |||| ||  ||| | ||||||    ||    | ||| |   ||   | |||                  |  ||  ||||       |||| ||||| ||||| || || ||||||||||||||||| ||  | ||| | |||||| ||||||| ||||||||||| ||||||||| || | ||||| |
gtatgcctttaaaacttcatctgttaaactggctattcttttcttttatagctgctaaacatgattctatgtcatggtattcctaatttgatcatttattccaacccttttcatcaatttttttcccatcagGTTGATGAACGGGCCGTTCTCAAGCACTTTGATTGGCCTGAAGGGAAAGCAGATGCATTAAGAGAAGCAGCCTTTGAATATCAAGACTTGATGAAATTGG

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|29646000|gb|CB651007.1|CB651007
EST:     GATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: GATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|29667941|gb|CB664216.1|CB664216
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|29612706|gb|CB617719.1|CB617719
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|157651193|gb|EX450827.1|EX450827
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTA                         GTCGATGAGCGGGCAGTAC
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTAC
EST: gi|29612723|gb|CB617736.1|CB617736
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|38475765|gb|CF959898.1|CF959898
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|29668095|gb|CB664370.1|CB664370
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|58609462|gb|CK037495.1|CK037495
EST:     ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAGCTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: ACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
EST: gi|29629417|gb|CB634426.1|CB634426
EST:     GTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTG                         GTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT
genomic: GTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACT

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), 75 (downstream exon)
Score: 105

TGTCGAGTCTCTAGCAAATGAGGTCCGAGCAGCAAGTTTTGTAAATATCGACGATGTTGTTGCATTTGTAAATTGGCTTGATGAGGAACTATCCTTCTTGgtaagcttat ... aacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG
                                         aaataac  putative branch site (score: 105)
                                       tcaaataacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttatctattttttttctatatgcaacacatgacaaaatagttagtactgaaaaagggtcaaataacattttagGTCGATGAGCGGGCAGTACTAAAGCACTTTGATTGGCCAGAGAGCAAAACTGATGCACTAAGAGAGGCAGCCTTTGAGTATCAAGACCTGCTAAAATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG