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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtattagtaaatgattgatgtgctctgatttcattgccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGGCTCCACCACCAA

Basic information

species Oryza sativa
transcript LOC_Os06g21390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g21390.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 2
gtaatgtattagtaaatgattgatgtgctctgatttcatt------gccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGGCTCCACCACCAA
|||| ||||||||||    |  |||   | |  | | |        |  | | | |  |||||| ||| ||| ||||  |||||| | |  |||     ||||||||||||| |||||||| |||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | |||||||   
gtaacgtattagtaa-cattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
















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|88402321|gb|CI596182.1|CI596182
EST:     AAGGAG--TACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
EST: gi|58606524|gb|CK034557.1|CK034557
EST:     AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTCTACCAGAAAGGTTCATGCTCCGTATGGTAGCCGTTGCCG
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTC-GTATGGTAGCCGTTGCCG
EST: gi|88344776|gb|CI624427.1|CI624427
EST:     AGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACCAAT                         GTTTGGACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCG
genomic: AGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAAC-AATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCG
EST: gi|88389034|gb|CI595268.1|CI595268
EST:     AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
EST: gi|88370752|gb|CI592518.1|CI592518
EST:     AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
EST: gi|88411921|gb|CI571413.1|CI571413
EST:     AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
EST: gi|88456027|gb|CI567743.1|CI567743
EST:     AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAAAAAT                         GTTTGCCCGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
EST: gi|58590312|gb|CF988620.1|CF988620
EST:     GGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTGCTAGCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCG
genomic: GGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTT-CTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCG
EST: gi|29659493|gb|CB655768.1|CB655768
EST:     AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT                         GTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA
genomic: AAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGA

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: 60 (upstream exon), 48 (downstream exon)
Score: 9

GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtatt ... acttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGGCTCCACCACCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGGCTCCACCACCAA
                                        ttcttac  putative branch site (score: 9)
                                        ttcttactt  CT-rich tract
              aaatctt  TA-rich tract