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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtattagtaaatgattgatgtgctctgatttcattgccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcag

Basic information

species Oryza sativa
transcript LOC_Os06g21390.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g21390.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G395842_T02 (Zea mays), 5'ss of exon 2
GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtattagtaaatgattgatgtgctctgatttcatt------gccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcag
 ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||| ||||||| |||| ||||||| ||||||||||    |  |||   | |  | | |        |  | | | |  |||||| ||| ||| ||||  |||||| | |  |||     |||||
AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtattagtaa-cattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcag
















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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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAATgtaatgtattagtaaatgattgatgtgctctgatttcattgccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcag

- - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - -  AGGAGA