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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttactttttggttttctcttcagaaggatgactttagtatctataactatcatagctatcattcactaaattttgaaaactggttctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTGGAATGAAGTTTTGCAATATCT

Basic information

species Glycine max
transcript GLYMA06G05900.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 6
gtaagttactttttggttttctcttcagaaggatgactttagtatctataactatcatagctatcattcactaaattttgaaaactggttctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTGGAATGAAGTTTTGCAATATCT
||||||| |       || |   ||  |           | || | ||  | || | |        ||  |||| | |||    |         | ||| ||| |||||||||| || || || || |||||||||||||| ||||||||||| || ||| | |||||  |
gtaagttgcgcgaaacttcttatttttg-----------tggtgttta--attaccgtgctcccagttttctaattgttgtgtgcc-------ctgcagGGACTTGGCACAGAACAAACTGAGTGGAGAGATACCAAGACTGATATATTGGAACGAGGTTCTTCAATACTT

upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttactttttggttttctcttcagaaggatgactttagtatctataacta-tcatagctatcattcactaaattttgaaaactggttctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTGGAATGAAGTTTTGCAATATCT
               || |  ||  ||      ||| | |   || | | |||| |  ||||||| ||     |   |           |||  || ||| ||| ||||||||||||| || || || ||||||||||||||||| || |||||||||||| | || |||||
---------------gtatgttcccca------tgattcttacatgtcttactacttttagctat-ataggtgatcatacatgtgtaatttcaattgcagGGACTTGGCACAGAATAAACTCAGTGGTGAGATACCAAGACTTATTTACTGGAATGAAGTTCTTCAGTATCT

upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttactttttggttttctcttcagaaggatgactttagtatctataactatcatagctatcattcactaaattttgaaaactggttctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTGGAATGAAGTTTTGCAATATCT
||||||| |  |||     ||   ||       |  | ||   || ||    | | ||  || |   ||| | | | || ||| |    |  ||||||| || |||||||||||||   | || || || ||||| || |||||||| ||||||||||||||||| |||||
gtaagtttccatttccacctcatctcc------tttccttctaatttaatgatgtaatgtct-tgggtca-tgactcttcaaagca---ttggttccagGGATCTGGCACAGAATAGATTGAGTGGAGAAATACCCAGGCTTATATACTGGAATGAAGTTTTGCAGTATCT

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|193578864|gb|FK536236.1|FK536236
EST:     ACCAATCCCTTCAACACTCTCTCAGGTTCCTAACTTGAAGATTCT                         AGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTG
genomic: ACCAATCCCTTCAACACTCTCTCAGGTTCCTAACTTGAAGATTCTgtaagttact ... tctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTG
EST: gi|208211558|gb|GE010911.1|GE010911
EST:     ATTGGACCAATCCCTTCAACACTCTCTCAGGTTCCTAACTTGAAGATTCT                         AGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTG
genomic: ATTGGACCAATCCCTTCAACACTCTCTCAGGTTCCTAACTTGAAGATTCTgtaagttact ... tctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTG
EST: gi|193419263|gb|FK382759.1|FK382759
EST:     ACACTCTCTCTAGGTTCCTAACTTGAAGATTTCT                         AGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATT
genomic: ACACTCTCTC-AGGTTCCTAACTTGAAGA-TTCTgtaagttact ... tctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctataactatcatagctatcattcactaaattttgaaaactggttctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTGGAATGAAGTTTTGCAATATCT
                        cactaaa  putative branch site (score: 2)
                                            ttctgttcc  putative PPT
                         actaaattttgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttactttttggttttctcttcagaaggatgactttagtatctataactatcatagctatcattcactaaattttgaaaactggttctgttccagAGACCTGGCACAGAATAATCTTAGCGGGGAGATACCAAGACTTATATATTGGAATGAAGTTTTGCAATATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT