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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcattctaagtctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt...

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 9
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgt---------atttaccaggctgtcattctaagtctctcgatcatctatatattgtgcacaaaggcactc----taatattatcaacatacgtgagtgtagc----aactgttttt--------------------------------------------
||| |||||||||||||| ||||| ||||| || || ||||| ||||| ||||| ||||||||| | ||||||||||||||||| ||||||||||||||||| |||| | | | ||| | | | | || | | | |||| | || | | || | | || | ||| | | || || |
TGCCATAATTGAGTACATACCTTTGTTGGCCAGCCAGTTAGGTGTTGGTTTTTTTGATGACAAGTTAGGGGCACTTTGCATGCAGTGGTTGGAAGATAAGgtgcataaataatttcaccaaccattattacacaagttccattaatgcagaaaccatgcatactatttctaatgatggtctttttagtctatataagttgaattcttgattgattctatgtaatgtaatagtgactcaaaataccaaacatttggcttcag

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 9
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggc-------tgtcattctaagt-ctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt
|||||| || || || || || |||||||| |||||||| || ||| | ||||||||||||||||| || || ||||||||||| ||||| | |||||||| | | | | || | | | || | | | || |||||| || | || | | ||| | || | || | |||||
TGCAATTATAGAATATATACCCTTATTGGCAAGTCAATTGGGGGTTAGTTTTTTCGATGACAAGCTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgacggtttt----tgttaaccaccttagttattgtag-----------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcattct--------aagtctctcgatcat-ctatatattgtgcacaaaggca------ctctaatattatcaacatacgtgagtgtagcaactgttttt-----
||| ||||| ||||| || ||||| ||||| ||||| ||||| ||||| || || || || ||||| || || ||||||||||||||||| |||| ||||||||| || || | || | | ||| || | | || | | | | | | | || | | | | | || || | |
TGCTATAATCGAGTATATCCCTTTGTTGGCAAGTCAGTTAGGTGTTGGCTTCTTTGACGATAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttttttttttttttttttttttttttttttttgcggatgctctcattag

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 9
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcatt-ctaagtctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt
|| ||||| ||||| ||||| || ||||| ||||||||||| || || || || ||||| ||||| || || ||||||||||||||||| |||| ||||| | || | | | | || | | || || |||| | || || || || | | | | | ||
GGCTATAATCGAGTATATTCCCTTGTTGGCCAGTCAATTAGGTGTAGGCTTCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtccctcattctctaccttcattgaatcatccagataaataaat-ttgtcgtctctactgcttgaaattttgaaataattataaat-tgtcag--------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggc------tgtcattctaagtctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt
||||||||| ||||| |||| | ||||| || || ||||| | |||||||||||||||||||| || || ||||||||||||||| || |||| ||||| | ||| ||| | |||| ||| | | |||||| | | | |||| | | | | ||
TGCAATAATAGAGTATGTTCCACTGTTGGCCAGCCAGTTAGGTATAGGATTTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAGgtttaccttgaatctttgatgtttgcataaatttctcattcacttgt-tattgtagatattgacactgttctcct-ccttcag-----------------------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 10
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcattctaagtctctcgatcatctata-tattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt--
||||||||| || |||||||||||| | || ||||| | || ||||| ||||| ||||||||||| || || ||||||||||||||||| |||||||||| | | | ||||| | |||||| || | | | || | | | | | |||| ||| | || | | | | |
TGCAATAATAGAATACATTCCTTTACTAGCAAGTCAGCTGGGTGTTGGTTTTTTTGATGACAAGCTTGGTGCTCTTTGCATGCAATGGTTAAAAGATAAGgt---cagtgaagttctagactaagagtaatgatcatgtaaaatgaattttacttgttcctttgactctgatcatcatccatgctcagaatagtttcctgttg

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcattctaagtctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgta-gcaactgttttt-----------------------------------------------------
||| |||||||||||||||||||||||||| || |||||||| || | ||||| || ||||| || || || || |||||||| ||| | |||||| |||| ||| | ||| | | | | | ||| || | || || | | || | | | ||| || || |||| |
TGCCATAATTGAGTACATTCCTTTATTGGCCAGCCAATTAGGTGTCGACTTTTTTGACGACAAACTAGGTGCTCTATGCATGCAGTGGCTTGAAGATCAGgttcttatattcccatcaagc--aatatgtggatgatttcta-atcacaagttgctgacttatatcgccaaagttgtcctcgagcttacacacctgtaccttaaggtttattcatatatttcttttaatcgtttttttttttttttttgaacag

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcattctaagtctct-cgatcatctatatattg-tgcacaaaggcactctaatat-tatcaacatacgtgagtgtagcaactgttttt---------------------------------
||| |||||||||||||| ||||||||||| || |||||||| || | |||||||| ||||| || || || ||||||||||| ||| | | |||| |||| || | ||| | | || || | | | | | | | || | || || || | | | | || | | ||| |||| ||
TGCCATAATTGAGTACATCCCTTTATTGGCCAGCCAATTAGGTGTGGACTTTTTCGACGACAAACTAGGCGCTCTTTGCATGCAGTGGCTTGGAGATCAGgttcatatattcccatcaagcaatgtttcgatggtggtttgtgtcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttag-aactagttcagtaatataatttcattcttttttggattaatag

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S117_137V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtc--attctaagtctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt--------------------------------------------------------------------------------------------
|| |||||||| ||||| ||||||||||| || ||||||||||||| ||||| |||||||| |||| ||||| |||||||| ||| | | ||| |||| || | || | || | | | ||| || | | || || | | | | | | | || |||| |
GGCCATAATTGAATACATACCTTTATTGGCCAGCCAATTAGGCGTTGACTTTTTTGATGACAAATTGGGAGCACTGTGCATGCAGTGGCTTGGAGACCAGgttcaaactttaccatctagtagtacatttgtggatttgttacgtgggatccattcttccaagttgtaggaagagtctttccttggaaaagatggtgttatatggacacagagtgagacgccagcttatcattttaaatatctacgtatttgagcccattttagtccaatctcattaaaagctaagctgcacag

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|29658916|gb|CB655191.1|CB655191
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|58683974|gb|CK072661.1|CK072661
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29641703|gb|CB646710.1|CB646710
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|38476835|gb|CF960968.1|CF960968
EST:     CGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAGTCGAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGA
genomic: CGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATC-AGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGA
EST: gi|87017349|gb|CI301385.1|CI301385
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29642127|gb|CB647134.1|CB647134
EST:     GCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: GCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|87038212|gb|CI192834.1|CI192834
EST:     ATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: ATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|87036423|gb|CI191045.1|CI191045
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29667131|gb|CB663406.1|CB663406
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|58685311|gb|CK073998.1|CK073998
EST:     TGGAAGATAAG                         TTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|218487576|gb|FG960599.1|FG960599
EST:     TTATCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGACGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTG
EST: gi|86899096|gb|CI296244.1|CI296244
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|33656227|gb|CF278841.1|CF278841
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|29621782|gb|CB626793.1|CB626793
EST:     TGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
EST: gi|58678838|gb|CK067525.1|CK067525
EST:     TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG
genomic: TTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttacca ... ttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAATAATTGAGTACATTCCTTTATTGGCTAGTCAATTAGGCGTTGGATTTTTCGATGACAAGCTGGGGGCACTTTGCATGCAATGGTTGGAAGATAAGgtatttaccaggctgtcattctaagtctctcgatcatctatatattgtgcacaaaggcactctaatattatcaacatacgtgagtgtagcaactgttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA