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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactgttgcccttcctgtctccagctctcatcgttgttcaggctgtaacaatattttttttatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG

Basic information

species Glycine max
transcript GLYMA10G28530.2
intron # 5
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 5
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------gtatgactgttgcccttcc-tgtctccagctctcatcg-ttgttcaggctgtaacaatattttttttatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG
                                                                     ||||  |||     ||   | |||     || || ||  || | |   ||||| | |||| ||||||| |   |||| || |||||||| ||||| ||||||||  |||||||||| || ||| |||| ||||| ||||||||||| |||
gtgtggtgttaattatttaaatttattttcattatggtctcttctatgttgtgtttttgcaaaagtctatatggttgtaaagtttaaatctctttttatcccagcggctgctgaaattgtaata-tattgtttttatttgatagATTTTCAGGGCATTGTCTTACATTCATCGCAGTATTGGAGTTTGTCATAGGGACATCAAACCTCAAAATCTTTTG

upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 4
gtatgactgttgcccttcctgtctccagctctcatcgttgttcaggctgtaacaatattttttttatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG
||| |  ||    | || || |  |||  ||      || | ||  |          ||| || |   | | |||| |   |  |  |  |||| || ||  |  | |||||||||||||| || ||||||||||| |||||| |||||
gtaagcttgcaagcgtttct-ttaccacttcc-----ttatccattcc-------cgtttcttct---tcgtagATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG
















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:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|23726962|gb|BU761494.1|BU761494
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATAT
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATAT
EST: gi|7926516|gb|AW832542.1|AW832542
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|151395928|gb|EV265805.1|EV265805
EST:     CTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: CTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|254344095|gb|GR851005.1|GR851005
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|16997089|gb|BM086461.1|BM086461
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|13311272|gb|BG404905.1|BG404905
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|151411363|gb|EV281174.1|EV281174
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|10843615|gb|BF066891.1|BF066891
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
EST: gi|6073128|gb|AW102515.1|AW102515
EST:     AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAG                         ATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG
genomic: AGTTGAACCAAAGGATGCCACTGATATATGTGAAACTCTATACATACCAGgtatgactgt ... tatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctccagctctcatcgttgttcaggctgtaacaatattttttttatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG
                           ctgtaac  putative branch site (score: 3)
                                    tatttttttt  putative PPT
                            tgtaacaatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgactgttgcccttcctgtctccagctctcatcgttgttcaggctgtaacaatattttttttatgttgcagATCTTTAGGGCATTATCTTATATTCATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG