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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATTGTCTGTATACTTGGAGAATCTTGCTACAACCCTTGGGTCCAGGGAACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcacttgtgttctatgtgtttacatactggatgacataaaatattaatgtgaagtgtgaccttgtgatgtcag

Basic information

species Oryza sativa
transcript LOC_Os04g46620.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 14
TGCATTGTCTGTATACTTGGAGAATCTTGCTACAACCCTTGGGTCCAGGGAACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgttt-gatcacttgtgttctatgtgtttacatactggatgacataaaatattaatgtgaagtg-tgaccttgtgatgtcag---
||| || || || ||| | ||||| ||||| || ||| | || ||  ||||||| ||||| ||||||||||| || ||||||||||||||||| |||||||||| ||||  || | |||||     ||| ||      |  ||  ||  |  |  |   ||   ||||||||      ||    
TGCGTTATCAGTTTACCTTGAGAACCTTGCAACGACCTTGGGTTCTCGGGAACAATTGGCAATTGCTGAATTTGCTGAATCTTTGTTAATCATACCAAAGgttttgatctgttctattctac----ttatatttcccttttcaccaatcaacatagcatagcaatgaccttgctgcaacaacag

upper sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G039263_T01 (Zea mays), 5'ss of exon 14
TGCATTGTCTGTATACTTGGAGAATCTTGCTACAACCCTTGGGTCCAGGGAACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgttt-gatcacttgtgttctatgtgt----ttacatactggatgacataaaatattaatgtgaag-tgtgaccttgtgatgtcag
|||  |||| || ||  ||||||| ||||| |||||||| || ||  ||||||| ||||| ||||||||||| || || |||||||||||||| |||||||||| ||||  || | || ||  |||    |||| |  |     |   || |||  | | | | |   |||||||| |    |||
TGCGCTGTCAGTTTATCTGGAGAACCTTGCAACAACCCTGGGTTCTCGGGAACAATTGGCAATTGCTGAATTTGCTGAGTCTTTGTTAATCATACCAAAGgttttgatctgttctattttacttgtagttttacttttttcgcaaatcaacatagcattttaatgacctgaccttgcgcctacag
















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|88225655|gb|CI225571.1|CI225571
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86492587|gb|CI135220.1|CI135220
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|88903572|gb|CI089110.1|CI089110
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|163920836|gb|EG710073.1|EG710073
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|38476533|gb|CF960666.1|CF960666
EST:     GGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCGAGGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: GGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86870800|gb|CI323844.1|CI323844
EST:     GTTAATCATTCCAAA-                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: GTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|88907485|gb|CI090279.1|CI090279
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|89198641|gb|CI016726.1|CI016726
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|88956051|gb|CI092339.1|CI092339
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|58677940|gb|CK066627.1|CK066627
EST:     AATCATTCCCAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCGAAGCTT
genomic: AATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86494033|gb|CI136666.1|CI136666
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|89180482|gb|CI044761.1|CI044761
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|88988240|gb|CI036200.1|CI036200
EST:     AATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86435769|gb|CI107002.1|CI107002
EST:     AATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|88218354|gb|CI218203.1|CI218203
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|27545689|gb|CA767120.2|CA767120
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGNTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAA-GATGCAACTGAACTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|88850339|gb|CI091832.1|CI091832
EST:     TTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: TTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|89180541|gb|CI044820.1|CI044820
EST:     GCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
genomic: GCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86514608|gb|CI157241.1|CI157241
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCGAAG                         GTTCTTTCTGTCAATGCTGCAGAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86415390|gb|CI069793.1|CI069793
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|58595799|gb|CK006327.1|CK006327
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|89175490|gb|CI042511.1|CI042511
EST:     TTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: TTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|86495901|gb|CI138534.1|CI138534
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT
EST: gi|58664881|gb|CK053567.1|CK053567
EST:     AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAG                         GTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCAAAGCTT
genomic: AACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTT

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), 65 (downstream exon)
Score: 42

TGCATTGTCTGTATACTTGGAGAATCTTGCTACAACCCTTGGGTCCAGGGAACAGTTGGCCATTGCTGAATTCGCGGAATCTTTGTTAATCATTCCAAAGgtttgatcac ... gtgatgtcagGTTCTTTCTGTCAATGCTGCAAAAGATGCAACTGAGCTTGTAGCCAAGCTTAGGGCATATCATCATACTGCTCAAACAAAGGCTGATAAGCAACACTTTT




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