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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattactaatatataacaataataataataattactttctctgctattcgctcgttgatcttcttctcttctggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG

Basic information

species Glycine max
transcript GLYMA19G27360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 1
gtaatta-ctaatatataacaataataataataattactttctctgctatt-cgctcgttgatcttcttctcttctggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG
||||  | |             |        |  || ||| | |  | |     |||      || || | | ||  || ||||||||||| | ||| | ||||||||||| || || ||||| |||||| |||||||||| || |||| ||||
gtaagcatcctccccgccttccttccttccttccttccttccgccaccaccatcctcaccctcctcctccgcctcccgcccgcagTTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAG

upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 1
-----------------------------------gtaattactaatatataacaataataataataattactttctctgctattcgctcgttgatcttcttct-cttctggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG
                                     |||  |    |   ||  ||    |  | ||   ||  |   ||    |      ||| || ||||  || ||| | ||||||||||| | ||  ||||||||||||| ||||| ||||| |||||| | |||||||||||||||| ||||
gtaatcctgtcgcttctcctcctccctccttccctccaatcgccggaaacgaatcatctagaacacaag-gctggcctcgcctcgcctgacctgacctccttccgctcctgccgcgcagTTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG

upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
gtaattactaatatataacaataataataataattactttctc-------tgctattcgctcgttga-tcttcttctcttctggct-cgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG
||||    |    | |  | |      |     | ||| || |       |    ||| | ||| |  ||  | | ||  |   || ||||||||||| | ||  | ||||||||||| ||||| ||||| || ||| |||||||||| ||||||| ||||
gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttctcgcgtcgcctcaccgtatccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG

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|7478459|gb|AW666273.1|AW666273
EST:     AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGA                         TTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTC
genomic: AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGAgtaattacta ... tggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTC
EST: gi|4294821|gb|AI442245.1|AI442245
EST:     AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGA                         TTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTC
genomic: AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGAgtaattacta ... tggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTC
EST: gi|298194875|gb|HO043347.1|HO043347
EST:     AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGA                         TTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTC
genomic: AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGAgtaattacta ... tggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTC
EST: gi|7925764|gb|AW831790.1|AW831790
EST:     AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGA                         TTCAACATTCCCAAC
genomic: AATTGCAGGAACGAATCTCCAAGCATTCCTTCGACACACCTCTCTACAGAgtaattacta ... tggctcgcagTTCAACATTCCCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataattactttctctgctattcgctcgttgatcttcttctcttctggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG
                          cgttgat  putative branch site (score: 5)
                        ctcgttgatcttcttc  CT-rich tract
     ttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattactaatatataacaataataataataattactttctctgctattcgctcgttgatcttcttctcttctggctcgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC