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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttctctttctcctaatctgcttgatgctaaatattgatgtggttcctttactggtatatggcctaagtatttgagtgtgtatgaatacag

Basic information

species Oryza sativa
transcript LOC_Os08g33440.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 4
GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttctctttctcctaatctgcttgatgctaaatattgatgtggttcctttactggtatatg-gcctaagtatttgagtgtgtatgaatacag
|||| ||||||||||| |||||||||||||||||||| ||| | ||||||||||| |||||||||||||||||| | ||   |   |      ||     ||| ||||   | |  ||  | |||  |   | |||| |  | | ||||||||| |   ||| | |||
GGACTTTTACACTGTCCAACTTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAGgtgggcttaaatccttttcttcctagaccatg-taaactgtaaaatgtatgcttcccatatgtatgagggttaatatttgagtatcactgagtgcag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 4
GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttctctttctcctaatctgcttgatgctaaatattgatgtggttcctttactggtatatggcctaagtatttgagtgtgtatgaatacag
|||| ||||||||||| ||| |||||||||||||||| ||| | ||||||||||| |||||||||||||||||| | ||   |   |      ||  |  ||| ||||   | || ||             || |  |  ||| |||| |||| |  |||| | |||
GGACTTTTACACTGTCCAACCTGGGTATGTTTGGTGTAGATCGGTTTGATGCAATCCTTCCACCTGGCCAGgtgggcttacttccttttcttcctagtctatg-taaactgtaatatgt-----------atacaaagattaa-tattcgagtatcaatgagtgcag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G24830.1 (Glycine max), 5'ss of exon 3
-----------------------------GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttctctttctcctaatctg----cttgatgctaaatattgatgtggttcctttactggta-tatggcctaagtatttgagtgtgtatgaatacag-----------
                             | || || || || || || |||||||||||||| ||||| || |||||||| || |||||||| |||||||| ||      |||||   | | ||    ||||||  | |    || ||||| || ||   ||| | | ||  |    ||| || | ||  |    | |             
TGACCCAAATTTAATTGTGCCTGCTACAGGAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatgatttctgggactttgaagtcttgat-ttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatttccag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 4
GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttctctttctcctaatctg----cttgatgctaaatattgatgtggttcctttactggta-tatggcctaagtatttgagtgtgtatgaatacag-----------
| || || || || || || |||||||||||||| ||||| || |||||||| || |||||||| |||||||| ||      |||||   | | ||    ||||||  | |    || ||||| || ||   ||| | | ||  |    ||| || | ||  |    | |             
GAACTTTCACGCTTTCCAATTTGGGTATGTTTGGAGTTGACAGGTTTGATGCCATACTTCCACCAGGCCAGgttagtgatgatttctgggactttgaagtcttgat-ttgagagatgttgtggctcattgtgtggcaatttgaacgttttatctgggggttcaactttgccctttatttccag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 4
GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttctctttc-----tcctaatctgcttgatgctaaatattgatgtggttcctttactggtatatggcctaagtatttgagtgtgtatgaata-cag
|||| || || ||||| || ||||| ||||||||||| || || |||||||| ||||| || ||||| |||||||| | |     |     |   |      ||  | |  || |||  | ||   | |||     | | ||  ||   | |   | | || |   ||  |||
GGACCTTCACTCTGTCCAATTTGGGCATGTTTGGTGTAGACAGGTTTGATGCTATTCTGCCTCCTGGTCAGgtgagttgcaaagccaggactttcacctctattagttcataagattcttctg-cccttttgggcatgtgtgagctttttctcaaaatttggaatgatgtcag

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|86498267|gb|CI140900.1|CI140900
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86502788|gb|CI145421.1|CI145421
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86836276|gb|CI346253.1|CI346253
EST:     TGTTTGGTCTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGGTGGTGGCTGATAA
genomic: TGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACA-GTGGTGGCTGATAA
EST: gi|58585893|gb|CF984201.1|CF984201
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|88740335|gb|CI763843.1|CI763843
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACC
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACC
EST: gi|88551307|gb|CI481352.1|CI481352
EST:     GTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: GTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86499821|gb|CI142454.1|CI142454
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86493670|gb|CI136303.1|CI136303
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|88531893|gb|CI458413.1|CI458413
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|88957325|gb|CI095286.1|CI095286
EST:     TTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|88248712|gb|CI248561.1|CI248561
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|27920911|gb|CB096719.1|CB096719
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86504491|gb|CI147124.1|CI147124
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86497312|gb|CI139945.1|CI139945
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86501999|gb|CI144632.1|CI144632
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86504362|gb|CI146995.1|CI146995
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86858948|gb|CI275150.1|CI275150
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|29663234|gb|CB659509.1|CB659509
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTTTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGGTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86597928|gb|CI276714.1|CI276714
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86499205|gb|CI141838.1|CI141838
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86501092|gb|CI143725.1|CI143725
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|88515702|gb|CI443356.1|CI443356
EST:     AGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGACATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: AGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|88224230|gb|CI224079.1|CI224079
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86504817|gb|CI147450.1|CI147450
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|66912791|gb|CX099639.1|CX099639
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86503803|gb|CI146436.1|CI146436
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86493073|gb|CI135706.1|CI135706
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86501837|gb|CI144470.1|CI144470
EST:     GGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCACACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: GGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTC-CACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
EST: gi|86859001|gb|CI276951.1|CI276951
EST:     TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAG                         GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA
genomic: TGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAA

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), 73 (downstream exon)
Score: 68

GGACATTTACACTGTCAAACTTGGGTATGTTTGGTGTTGATAGATTTGATGCAATTCTTCCACCTGGCCAGgtgaggttct ... atgaatacagGGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAAGATGGTTTCTTTAGTGTCAAGAGCAAAATGCTG




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