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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactagctagtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT

Basic information

species Oryza sativa
transcript LOC_Os02g01340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059191_T01 (Zea mays), 3'ss of exon 2
--------gtaactagcta--gtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT
        |||  ||  |    || |  |||   |||   | ||||   |  || |  | || |   ||| | |||  |  |  |   |||      |   |||||||||| |||||||||||||| || ||||||||||||||||| ||||| ||||||||||||||||| |||||||| |
gcttgtatgtacatatttgttatattaatttatatgcagga-cgattctattcaaattaaattaa--aacaatcataaaagttttttgtgagtatatgtgtagGTATCGCTTTGCGTGAAGAGGCTAGTCTACACCAACGATCAGGGGGAGATTGTCAAAGGAGTCTGCTCAAACTTCCTGT

upper sequence: LOC_Os02g01340.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059083_T02 (Zea mays), 3'ss of exon 2
gtaactagctagtagt--gtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT
      ||| | |  |   |     ||  |  ||  ||   |   |     ||  |   |  || |   | || | |      | ||| |  ||||| ||||||||||||||||||||||| ||||||||||||||||| ||| ||||||||||||||||||| ||||||||||
---gtgagccaatgattaatacaaattaattaattaattatatgtatgtatcaccattaagatagctatggcaactttt---gttgat-gtgcagGTGTCGCTGTGCGTGAAGAGGCTGGTCTACACCAACGATCAGGGGGAGGTCGTCAAAGGAGTCTGCTCGAACTTCCTCT
















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|38479097|gb|CF963230.1|CF963230
EST:     CTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACT-CAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: CTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|25798321|gb|CA754282.1|CA754282
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCNAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|33656206|gb|CF278820.1|CF278820
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGGCTGGTGTACACCAACGATCAGGGGAGAGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGG-CTGGTGTACACCAACGATCAGGG-AGAGA
EST: gi|4880924|gb|AU065223.1|AU065223
EST:     TCTACTCCATCGCCAGCANCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTG-GTGAAGAGGCTGGTGTACACCAA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAA
EST: gi|8956400|gb|BE230203.1|BE230203
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58595302|gb|CF993610.1|CF993610
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGAT
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGAT
EST: gi|58611960|gb|CK039672.1|CK039672
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACAC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACAC
EST: gi|29676003|gb|CB672278.1|CB672278
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58594835|gb|CF993143.1|CF993143
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAG
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAG
EST: gi|58588294|gb|CF986602.1|CF986602
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58662943|gb|CK051629.1|CK051629
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|38477836|gb|CF961969.1|CF961969
EST:     TCTACTCCAGCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|33817858|gb|CF334761.1|CF334761
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACGCCAACGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATC
EST: gi|58588807|gb|CF987115.1|CF987115
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGA
EST: gi|33653470|gb|CF276084.1|CF276084
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATTCGCTGTGCGTGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTAT-CGCTGTGCGTGA
EST: gi|33661411|gb|CF292378.1|CF292378
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|58607665|gb|CK035698.1|CK035698
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTG
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTG
EST: gi|8956756|gb|BE230559.1|BE230559
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATAAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|33661543|gb|CF292510.1|CF292510
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATC
EST: gi|33662396|gb|CF293363.1|CF293363
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|29658349|gb|CB654624.1|CB654624
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATC
EST: gi|44677984|gb|CR291418.1|CR291418
EST:     TCTACTCCATCGCCAGCAGCGCCATCGGGGATTTCGCCGACTCCAAGACG                         GTATCGCTGTGCGTGAAGA
genomic: TCTACTCCATCGCCAGCAGCGCCATCGGGGACTTCGCCGACTCCAAGACGgtaactagct ... gatcgatcagGTATCGCTGTGCGTGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT
                  taactaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactagctagtagtgtttttcttgctccatcgatctcaaccacaagacatgagctaactaacatcgacatcgtccctgatcgatcgatcagGTATCGCTGTGCGTGAAGAGGCTGGTGTACACCAACGATCAGGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG