Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcttcggttgcatccgcatttctatatttccccacttgcactgttctaccatcttgcttgcttatgttacactgtctatgaaccacatcaaatgaggtgatgtaatcatggtgcatatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTACGCGCTTGATAGGATCTGGAAAGATATAGGAACCTATCGGAATGTGGAC

Basic information

species Oryza sativa
transcript LOC_Os11g39220.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G820287_T02 (Zea mays), 3'ss of exon 6
gtaaattcttcggttgcatccgcatttctatatttccccacttgcactgttctaccatcttgcttgcttatgttacactgtctatgaaccacatcaaatgaggtgatgtaatcatggtgcatatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTACGCGCTTGATAGGATCTGGAAAGATATAGGAACCTATCGGAATGTGGAC
                               |  ||  || |   |    | |  ||  |   |||       |||  ||||  |  ||     | |     |  |   | | | | ||||||||||||| ||||| || |||||| | |||||| | |||||  |||| ||||||||||| ||||| || ||||||||| ||||||| ||||| ||||||||||| |||
--------------------------aaggcagctcgtcattcagatgcctttcacacatcttttga----aatactttgtcacttcactgtgaccacaattgacaaacacttacgatgcatatatgcagCTGCCCTGACGAAAAATCGCGGGAAGTATTGAAGCTGGTATGCGACCTTTATGCGCTCGACAGGATCTGGCAAGATATCGGAACGTATCGGAATGTAGAC

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G099666_T01 (Zea mays), 3'ss of exon 5
gtaaattcttcggttgcatccgcatttctatatttccccacttgcactgttctaccatcttgcttgcttatgttacactgtctatgaaccacatcaaatgaggtgatgtaatcatggtgcatatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTACGCGCTTGATAGGATCTGGAAAGATATAGGAACCTATCGGAATGTGGAC
                               |  ||  || |   |    | |  ||  |   |||       ||| ||| |  |  ||     | |     |  |   | | |   ||||||||||||| ||||| || |||||| |||||||| | |||||  |||| ||||||||||| ||||| || ||||| ||| ||||||| ||||| ||||||||||| |||
--------------------------aaggcagctcgtcattcagatgcctttcacacatcttttga----aatactctggcacttcactgtgaccacaattgacaaacacttacaatgcatatatgcagCTGCCCTGACGAAAAATCACGGGAAGTATTGAAGCTGGTATGCGACCTTTATGCGCTCGACAGGATTTGGCAAGATATCGGAACGTATCGGAATGTAGAC

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G445791_T01 (Zea mays), 3'ss of exon 6
gtaaattcttcggttgcatccgcatttctatatttccccacttgcactgttctaccatcttgcttgcttatgttacactgtctatgaaccacatcaaatgaggtgatgtaatcatggtgcatatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTACGCGCTTGATAGGATCTGGAAAGATATAGGAACCTATCGGAATGTGGAC
                               |  ||  || |   |    | |  ||  |   |||       |||  ||||  |  ||     | |     |  |   | | | | ||||||||||||| ||||| || |||||| |  ||||| | |||||  |||| ||||||||||| ||||| || ||||||||| ||||||| ||||| ||||||||||| |||
--------------------------aaggcagctcgtcattcagatgcctttcacacatcttttga----aatactttgtcacttcactgtgaccacaattgacaaacacttacgatgcatatatgcagCTGCCCTGACGAAAAATCGTGGGAAGTATTGAAGCTGGTATGCGACCTTTATGCGCTCGACAGGATCTGGCAAGATATCGGAACGTATCGGAATGTAGAC

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|86256651|gb|CI061414.1|CI061414
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|58693190|gb|CK081877.1|CK081877
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|9865504|gb|AU101254.1|AU101254
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|86436185|gb|CI117907.1|CI117907
EST:     TCACACCTTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCCAAAG                         ATGCCCGGATGAAAAAACCCGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|88227777|gb|CI227257.1|CI227257
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29685887|gb|CB682162.1|CB682162
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29639954|gb|CB644963.1|CB644963
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGCCCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|86539202|gb|CI179408.1|CI179408
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|88342477|gb|CI645999.1|CI645999
EST:     GTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: GTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|87019925|gb|CI299323.1|CI299323
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|218487621|gb|FG950218.1|FG950218
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29678644|gb|CB674919.1|CB674919
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29678051|gb|CB674326.1|CB674326
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|86522635|gb|CI162841.1|CI162841
EST:     TGCGAAGTTCATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29645622|gb|CB650629.1|CB650629
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29633508|gb|CB638517.1|CB638517
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29642868|gb|CB647875.1|CB647875
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|88830894|gb|CI079328.1|CI079328
EST:     AGTCTGTCATTCTTGCGAAGTTAATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: AGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29626585|gb|CB631596.1|CB631596
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29680960|gb|CB677235.1|CB677235
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29669185|gb|CB665460.1|CB665460
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|89188395|gb|CI115644.1|CI115644
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCCAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29642215|gb|CB647222.1|CB647222
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29662988|gb|CB659263.1|CB659263
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|42591851|gb|CK738337.1|CK738337
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29676319|gb|CB672594.1|CB672594
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29641783|gb|CB646790.1|CB646790
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|88216181|gb|CI216030.1|CI216030
EST:     TAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29631514|gb|CB636523.1|CB636523
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29624634|gb|CB629645.1|CB629645
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGCCCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29668162|gb|CB664437.1|CB664437
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
EST: gi|29684386|gb|CB680661.1|CB680661
EST:     TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAG                         ATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA
genomic: TCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattctt ... atatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgtctatgaaccacatcaaatgaggtgatgtaatcatggtgcatatatgcagATGCCCGGATGAAAAAACACGGGAATTGTTGAAATTGGTGTGCGACCTTTACGCGCTTGATAGGATCTGGAAAGATATAGGAACCTATCGGAATGTGGAC
                                             atatat  TA-rich tract