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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTATTGGAGGTGGTCAAGATGCGATGAATGTGACTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttag

Basic information

species Oryza sativa
transcript LOC_Os08g21660.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g21660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 5
GTGGTTATTGGAGGTGGTCAAGATGCGATGAATGTGACTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttag-
|||||| | ||||||||||| ||||| ||||||||||||||||| || || ||||| || |||||||| || ||||| |  |||||||| | || |  |  || ||  |  |    |||  ||| |            | | | | || |||| ||   ||| | | |    || ||  || |   ||  |  ||  |||||   
GTGGTTCTAGGAGGTGGTCAGGATGCAATGAATGTGACTATGACTGACCGCCGTGCTGGTAAATTTGAGGCTAAATTCTACCACAAGgtgatttttcagttcacagaatataa---atgccttactctttttgtgttacatcttgctaactttgcatgcttacaatat----ttgaaccattattattaaaacttgctcttttag

upper sequence: LOC_Os08g21660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G028834_T03 (Zea mays), 5'ss of exon 5
GTGGTTATTGGAGGTGGTCAAGATGCGATGAATGTGACTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttcttcg-cacatagtttccatcttatgttttagtgagaaca-atgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttag
|||||| | ||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || || ||||| | ||||||||| | |||||   ||  || |         | |  ||| |         | |     | | || |||   | | ||| | |||  ||  |     |||        |  | |  |||||
GTGGTTCTAGGAGGTGGTCAGGATGCAATGAATGTGACTATGACAGATCGCCGTGCTGGTAAATTCGAGGCTAAATTCTATCACAAGgtaatttctttttcagttaataaattatcaaggcattactccttttgtgttacttccttgctaacttggtatacttacaattt-ttgaactgttctgattaaaacttgctctcttttag
















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|29637698|gb|CB642707.1|CB642707
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|89174599|gb|CI110797.1|CI110797
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTGTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCCTTTTGGACCCATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86428041|gb|CI073138.1|CI073138
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86539171|gb|CI179377.1|CI179377
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|427350|gb|D23414.1|D23414
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88552964|gb|CI483028.1|CI483028
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88534415|gb|CI463136.1|CI463136
EST:     ACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: ACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88983105|gb|CI020669.1|CI020669
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|87015288|gb|CI275478.1|CI275478
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86866716|gb|CI343538.1|CI343538
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86255807|gb|CI066870.1|CI066870
EST:     GGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: GGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|89193673|gb|CI116306.1|CI116306
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88296843|gb|CI540195.1|CI540195
EST:     TCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: TCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88557329|gb|CI487726.1|CI487726
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCNAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTGTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86896321|gb|CI330184.1|CI330184
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86494802|gb|CI137435.1|CI137435
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|10794823|gb|AU108789.1|AU108789
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCNCAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGNCCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86495775|gb|CI138408.1|CI138408
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|218499018|gb|FG959220.1|FG959220
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGGGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88222839|gb|CI220690.1|CI220690
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86419096|gb|CI053897.1|CI053897
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|2797339|gb|AA750633.1|AA750633
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|33794412|gb|CF323090.1|CF323090
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|86419296|gb|CI054097.1|CI054097
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
EST: gi|88549198|gb|CI479063.1|CI479063
EST:     CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAG                         ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC
genomic: CTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttctt ... ttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTATTGGAGGTGGTCAAGATGCGATGAATGTGACTATGACAGATCGTCGTGCAGGAAAATTTGAAGCGAAATTTTTTCACAAGgtcagttcttcgcacatagtttccatcttatgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC