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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgcaacaccggctgacatatgacatgcgtagacgaaaatttctgaaccaccgatcaacttataattatctactaatctggccgatttgaacag

Basic information

species Oryza sativa
transcript LOC_Os05g04340.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA02G01220.1 (Glycine max), 5'ss of exon 12
GAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgcaacaccggctgacatatgacatgcgtagacgaaaatttctgaaccaccgatcaacttataattatctactaatctggccgatttgaacag
|| || |||   || || ||||| |||||||| ||||||||||| || ||| |||| || || |||| |||||| || ||||| |||||||   || ||||||||     |    | | ||| |||| |  | | |  |      | | | |      |   ||     |  |  |   |  |||| |  |         
GAGGCCTTGGCTCACCCATTCTTTGATGAACTGCGTGATCCAAATACTCGCCTACCAAATGGGCGTTACCTTCCCCCACTCTTTAACTTCAGAGCCAATGgtaagaactaattctctgatga-atattatgttcttgtatccttttatttaattgcttgtgtaatgctgatgttgccggtgttctgacacag--------

upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G01280.2 (Glycine max), 5'ss of exon 12
GAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgcaacaccggctgacatatgacatgcgtagacgaaaatttctgaaccaccgatcaacttataattatctactaatctggccgatttga-acag
|| || ||| | ||||| ||||| |||||||| ||||||||||| |||||| |||| || || |||| |||||| || ||||| |||||||   || ||||||||     ||  |   |||||| ||    ||| |    | |   || |     |  | |    | ||      ||  |  |   |  | | ||| ||||
GAGGCCTTGGTTCATCCATTCTTTGATGAACTGCGTGATCCAAATACCCGCCTACCAAATGGGCGTTACCTTCCCCCACTCTTTAACTTCAGAGCCAATGgtaagaac-taattct--ctgacaaatat--tgcatttgtgtatccttttatttaattgcttgtgtgatg-----ctgatgttgccggtgttctgacacag

upper sequence: LOC_Os05g04340.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 5'ss of exon 12
GAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgta-agcttgcaacaccggctgacatatgacatgcgtagacgaaaatttctgaaccaccgatcaacttataattatctactaatctggccgatttgaacag
|| || |||||||||||||| || ||||| || ||||| |||||||||||  | || || || ||||||||||| ||  | |||||||||||||| ||||||| |  ||     |        | | |  |     |  |    | |     ||   | || |||  | |  |||| | ||  |  | | |||  |     
GAGGCTTTGATCCATCCCTTTTTTGATGAGCTACGTGAGCCAAACACCCGTCTGCCAAATGGACGTTTCCTTCCCCCATTGTTCAACTTCAAGCCTCATGgtacaaattattttaaaattattctttttgctgttttttatcccagtg---aaatggctgaccaatgt-ttgttat-tgctgcttcgactgatcag-----

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|29629993|gb|CB635002.1|CB635002
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|33798704|gb|CF325210.1|CF325210
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|29629559|gb|CB634568.1|CB634568
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|86256515|gb|CI061278.1|CI061278
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|88849654|gb|CI089760.1|CI089760
EST:     CGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTNATCCCCGAACATG
genomic: CGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|25804076|gb|CA760037.1|CA760037
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|86251622|gb|CI016911.1|CI016911
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|86482760|gb|CI125393.1|CI125393
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|51946083|gb|CV152424.1|CV152424
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|86425762|gb|CI070859.1|CI070859
EST:     GAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: GAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|29623769|gb|CB628780.1|CB628780
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|88845458|gb|CI084383.1|CI084383
EST:     ACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: ACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|88839091|gb|CI378015.1|CI378015
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|87024245|gb|CI256986.1|CI256986
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|86433457|gb|CI093800.1|CI093800
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
EST: gi|88828410|gb|CI073280.1|CI073280
EST:     CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATG                         AACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG
genomic: CTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATG

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

GAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgc ... atttgaacagAACTGAAGGGTATGCCAATGGAATTCCTGGTGAAGCTTATCCCCGAACATGCTCGAAAGCAATGCGCGTTTGTAGGATGGTGATTTCTGAGGTCAGCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCATTGATCCATCCCTTCTTCGATGAACTCCGTGATCCAAACACCCGCTTACCGAACGGCCGTTTCCTTCCTCCTCTCTTCAACTTCAAGCCCCATGgtaagcttgcaacaccggctgacatatgacatgcgtagacgaaaatttctgaaccaccgatcaacttataattatctactaatctggccgatttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC