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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggactttgttttaatttgcataaatcattgataatttattctgattctcttgtttcatagttatggttgtgtttaggggagctaaaagatgggaagcaactaattcaaactctgcagacagggctgttgggtggaaaatactaactgaatgtttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG

Basic information

species Glycine max
transcript GLYMA10G28530.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 6
gtatggactttgttttaatttgcataaatcattgataatttattctgattctcttgtttcatagttatggttgtgtttaggggagctaaaagatgggaagcaactaattcaaactctgcagacagggctgtt-gggtggaaaatactaactgaatgtttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG
                                                       ||  |||||||    |  |||| | |     ||  || | | |  | ||  |||  ||  |     |||    ||||   ||  |||||  |       |  || |||||| |||| |||||||| || |||||| ||||  |||||||||||||||||||||| || |||
----------------------------------------------------acagtcgcatagtttccatattgttaatga----tatgagtttgtattccac--attgcaatgc-----acaattttgttcaagtaaaaaattttg------ttcttctctgtgtagGTGAATCCACATACCCACCAGCTTAAGCTATGTGACTTTGGAAGTGCAAAAGTCTTG
















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|13312851|gb|BG406502.1|BG406502
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|7926516|gb|AW832542.1|AW832542
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTNTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|151395928|gb|EV265805.1|EV265805
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|254344095|gb|GR851005.1|GR851005
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTAT-G                         GTCAATCCACACACTC
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTC
EST: gi|16997089|gb|BM086461.1|BM086461
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|6566727|gb|AW234359.1|AW234359
EST:     GGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: GGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|13311272|gb|BG404905.1|BG404905
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|151411363|gb|EV281174.1|EV281174
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|10843615|gb|BF066891.1|BF066891
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|6073128|gb|AW102515.1|AW102515
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|7926372|gb|AW832398.1|AW832398
EST:     GGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: GGGATATCAAGCCTCAAAATCTATTGgtatggactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgcagacagggctgttgggtggaaaatactaactgaatgtttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG
                             tactaac  putative branch site (score: 0)
                                        tgtttttct  putative PPT
                         aaaatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggactttgttttaatttgcataaatcattgataatttattctgattctcttgtttcatagttatggttgtgtttaggggagctaaaagatgggaagcaactaattcaaactctgcagacagggctgttgggtggaaaatactaactgaatgtttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG