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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttctatcctcatacaaatgtgccagaaattattggtttcatgatatttactgctgtatcactttaacag

Basic information

species Oryza sativa
transcript LOC_Os04g58580.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58580.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G165535_T05 (Zea mays), 5'ss of exon 9
GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttcta---------tcctcatacaaatgtgccagaaattattggtttcatgatatttactgctgtatcactttaacag-----
|| |||||||| || ||||||||||| |||||||||||||||||||| || ||| ||||||||||||||||||| ||||||||||||||||||||||| || || |||         | |   ||   || | |  ||||| ||||   |||||| |||||||  ||   ||||  || |      
GTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGATgtgagtctcctagaccaccagtacatgtatttattttcttgaaatgattgaaatcatgacatttactaatgc--cactaaaaaattccag

upper sequence: LOC_Os04g58580.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA09G39800.1 (Glycine max), 5'ss of exon 9
GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttctatcctcatacaaatgtgccagaaattattggtttcatgatatttactgctgtatcactttaacag----------
|| || ||||| || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| || |||||||| ||||| ||||||||||||||   |  ||  ||||    |||    ||  ||| |   |||  |||||  |       | | | |||||             
GTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGATgtaagtaata-attttcatg-gcatgatgtagtgattttatttttggtgataagtcaacagatcttaatttaaatatactccccag

upper sequence: LOC_Os04g58580.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA18G46390.1 (Glycine max), 5'ss of exon 9
-GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttctatcctcat-aca-aatgtgccagaa--attattggtttcatgatatttactgctgtatcactttaacag---------
 || || || || || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| || |||||||| ||||| ||||||||||||||   |  ||  |||| |||  |||||        ||| ||| |    ||||| ||      ||   | |||||            
GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAtgtaagtaatg-attttcatgacatgatgtggtgattttatttttgataaagtgatagttcaacaggtcctaatttaaatatactccaca

upper sequence: LOC_Os04g58580.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 5'ss of exon 8
GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc---------tatcctcatacaaatgtgccagaaattattggtt-tcatgatatttactgctg----tatcactt-taacag
 | || ||||| || || || ||||| || ||||||||||| ||||| || ||| | ||| ||||||||||||||||||| || || || |||||||| ||  | |         |||  |       |||   |  ||| || |     | |    || || |||||    ||   ||| | ||||
ATTCACAACATACGTCCGAAGATGGTTTCTGTGCTTCGTGAGAAGTTTGCTCACCTAAACCTGACATTTTCTATTGGAGGACAAATAAGCTTTGATgtgagtgtccattcatctttatttttgctttgatgattcgaaaactagtatcaatgactgaatgtattgctggtcataatgcttgtgacag

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|88479882|gb|CI417153.1|CI417153
EST:     TTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|29627056|gb|CB632067.1|CB632067
EST:     TCGCCCACTTGAACTTGACATTTTTTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88474449|gb|CI411720.1|CI411720
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88472220|gb|CI409491.1|CI409491
EST:     CATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: CATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|58604165|gb|CK014693.1|CK014693
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88248182|gb|CI248031.1|CI248031
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|29641676|gb|CB646683.1|CB646683
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|86547064|gb|CI187270.1|CI187270
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88484906|gb|CI422177.1|CI422177
EST:     CTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: CTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88846893|gb|CI005872.1|CI005872
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88479864|gb|CI417135.1|CI417135
EST:     CTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: CTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88376207|gb|CI533109.1|CI533109
EST:     AACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: AACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|8859293|gb|AU096611.1|AU096611
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88510400|gb|CI437906.1|CI437906
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|88545595|gb|CI475164.1|CI475164
EST:     TTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|86886810|gb|CI334724.1|CI334724
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
EST: gi|86542297|gb|CI182503.1|CI182503
EST:     TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT                         GTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA
genomic: TCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttc ... actttaacagGTGTTCCCACAAGGCTGGGACAAAACTTACTGCTTGAGATATCTTGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGATgtaagccttctatcctcatacaaatgtgccagaaattattggtttcatgatatttactgctgtatcactttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT