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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctattaatatgattgttagcaatatgtttttacttctgttttcatggtttcagctgtcttatcacttatttagttaaatctttcttttgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTGGTGTTGTTCGCCTGGCTCAAGTAAATATGGAACTGGCTAGGATTGAAGC

Basic information

species Glycine max
transcript GLYMA05G04170.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G04170.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g48410.1 (Oryza sativa), 3'ss of exon 4
-attctattaatatgattgttagcaatatgtttttacttctgttttcatggttt-cagctgtcttatcacttatttagttaaatctttcttttg--ctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTGGTGTTGTTCGCCTGGCTCAAGTAAATATGGAACTGGCTAGGATTGAAGC
 ||| ||||    |||    |        ||   |  || |||||   ||     || || |  ||| |       | |||| ||  |    |    | | |||| || ||| |||||||||||||  | || |||||||| || | ||| |||||||||||||| ||||||||||| ||||||||| ||||||   |||||||
tattgtattttcctgaggcatgattgctggtcagt-tttttgtttatgtgacgcacacctattctattatgag---aattaattccatgcactaacttctgcagATTTTTTAGTATCTGCTGCTGTAGCTGAGTTCAAAGGGCCTGTTATATTTGGTGTTGTTCGTCTGGCTCAAGTTAATATGGAATTGGCTATAGTTGAAGC

upper sequence: GLYMA05G04170.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G175728_T01 (Zea mays), 3'ss of exon 4
--attctattaatatgattgttagcaatatgtttttacttctgttttcatggtttcagctgtcttatcacttatttagt--taaatctttcttttgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTGGTGTTGTTCGCCTGGCTCAAGTAAATATGGAACTGGCTAGGATTGAAGC
   | |  | |   || |||   |   ||| ||  || |      | ||| ||||    | | |||  ||| |||  ||  |    |   |   |    | |||| |||||| | |||||||||||  | || || ||||| || | | | |||||||||||||| ||||| |||||||| |||||  |||||||  |||||||
gactaccttcagattgcttgcctgttctattttgctaatatg--ctgcatagttttg--tatattaggactaattctgtgctcccccccccccctaacatgcagATTTCTTAGTTTCTGCTGCTGTAGCTGAGTTTAAAGGGCCTGTTGTATTTGGTGTTGTTCGTCTGGCCCAAGTAAACATGGAGTTGGCTAGAGTTGAAGC

upper sequence: GLYMA05G04170.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g04830.t01 (Vitis vinifera), 3'ss of exon 4
attctattaatatgattg--ttagcaatatgttt--ttacttctgttttcatggtttcagctgtcttatcacttatttagttaaatcttt-cttttgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTGGTGTTGTTCGCCTGGCTCAAGTAAATATGGAACTGGCTAGGATTGAAGC
     || |||||  ||   | |    | |||||  |  |||    ||   |      |    ||  |   |  | ||  || |  | || || | | | |  ||| || ||  | |||||||||||| | ||||||||||||||||||||||| ||||| |||||| |||||||||| ||||||||| ||||||||||||||||
-----atcaatatagttcattcacttctgtgtttgatggctttcagttctcttacaaaaataatcagagttcgcaattcattgaccccttgctatcgttctgtagATTTTTTGGTTTCTGCTGCTGTTGCTGAATTCAAAGGTCCAGATATTTTCGGTGTGGTTCGCTTGGCTCAAGTGAATATGGAATTGGCTAGGATTGAAGC

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|15813872|gb|BI786147.1|BI786147
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|208102597|gb|GD899718.1|GD899718
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGGAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|7925023|gb|AW831049.1|AW831049
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|19348018|gb|BM892550.1|BM892550
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|192323242|gb|FK017408.1|FK017408
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|208239928|gb|GE042696.1|GE042696
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGGAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|298193290|gb|HO033724.1|HO033724
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|31560990|gb|CD486828.1|CD486828
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|23729206|gb|BU762690.1|BU762690
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|12773216|gb|BG238143.1|BG238143
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|298197805|gb|HO039344.1|HO039344
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGC
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGC
EST: gi|15813113|gb|BI785388.1|BI785388
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGCCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|9898846|gb|BE607814.1|BE607814
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTATG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|7925605|gb|AW831631.1|AW831631
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGGTTCCGAATTCAGAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|208032075|gb|GD828517.1|GD828517
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGGAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|208087538|gb|GD890218.1|GD890218
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGGAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
EST: gi|298163073|gb|HO011806.1|HO011806
EST:     GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAG                         ACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG
genomic: GGAGCAGACTGGTAGAAAAGCCCGGTTAATTGGACAAGGAGTGCCGGAAGgtttgccgat ... tgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggtttcagctgtcttatcacttatttagttaaatctttcttttgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTGGTGTTGTTCGCCTGGCTCAAGTAAATATGGAACTGGCTAGGATTGAAGC
                                    tctttcttttgcttta  CT-rich tract
                       ttatttagttaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctattaatatgattgttagcaatatgtttttacttctgttttcatggtttcagctgtcttatcacttatttagttaaatctttcttttgctttacagACTTCTTAATATCTGCTGCTGTTTCCGAATTCAAAGGTCCAGATATTTTTGGTGTTGTTCGCCTGGCTCAAGTAAATATGGAACTGGCTAGGATTGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - acttctg
- - - - - - - - - - - - - - - - - - - - - -ttcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -cagctgt