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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATAGCCTTGTCTGCCAAAGCGCTTTAGACCGACTGCATAGAACCAGGGAGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatctttttcatatggctcacaagaaaacttgccttgttacaaatgctatttttattctgggtaagatttctgtttttcacaaaatacatgagac...

Basic information

species Oryza sativa
transcript LOC_Os03g48300.1
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G022997_T02 (Zea mays), 5'ss of exon 3
GGATAGCCTTGTCTGCCAAAGCGCTTTAGACCGACTGCATAGAACCAGGGAGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatctttttcatatggctcacaagaaaacttgccttgttacaaatgctatttttattctgggtaagatttctgtttttcacaaaatacatgagac---
||| |||||||||||||| || ||||| ||||| || |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||| |  |||||||||||||||| |||     |     |    ||   |   | |   |   |  |  |||  ||| |   || | | | |||| ||        |  ||   
GGAAAGCCTTGTCTGCCAGAGTGCTTTGGACCGTCTACATAGAACTAGGGAGCTTGATTACATGAGTAATATTGTGCTTAGAATGTTTGAAAACATAGAGgtatggatctttt-catcatctttgtctggtctctgaacagataattcacctttctggtatagtgg-tcgtatatatatatttc-catctcgtgcggtacaag
















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|58605143|gb|CK033176.1|CK033176
EST:     ATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: ATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|29672858|gb|CB669133.1|CB669133
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|88974007|gb|CI002669.1|CI002669
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|89168931|gb|CI020471.1|CI020471
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|86827434|gb|CI272827.1|CI272827
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|88844694|gb|CI021269.1|CI021269
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|29674286|gb|CB670561.1|CB670561
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|29640071|gb|CB645080.1|CB645080
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|29645913|gb|CB650920.1|CB650920
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|29645535|gb|CB650542.1|CB650542
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|88839229|gb|CI000701.1|CI000701
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAGGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|86902835|gb|CI312212.1|CI312212
EST:     AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: AGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|86252520|gb|CI003856.1|CI003856
EST:     TATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
genomic: TATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGT
EST: gi|86885163|gb|CI316923.1|CI316923
EST:     CATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAG                         GTTCCTTTAGAAGATGAGAAAAGGTTCCGGAGTGAAATGACATTTAGGTCG
genomic: CATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTA-GTCG

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: 53 (upstream exon), 60 (downstream exon)
Score: 14

GGATAGCCTTGTCTGCCAAAGCGCTTTAGACCGACTGCATAGAACCAGGGAGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatct ... gtatttacagGTTCCTTTAGAAGATGAGAAAAGGTTCCGGATTGAAATGACATTTAGTCGTGGTGCTGATCTTAGTCCTCTAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAGCCTTGTCTGCCAAAGCGCTTTAGACCGACTGCATAGAACCAGGGAGCTTGACTACATGAGTAATATTGTGCTTAGAATGTTTGAAAATACTGAGgtatggatctttttcatatggctcacaagaaaacttgccttgttacaaatgctatttttattctgggtaagatttctgtttttcacaaaatacatgagac

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