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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag

Basic information

species Glycine max
transcript GLYMA16G06100.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 4
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtag-aatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag
|| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||||| |   || ||     ||| ||      |   |   | | |     |||  || | |  |  | |  |   ||                            
GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataacatctgtcattatgtgcatttctcatctcctttggtttcttg-ctctgacaccttcatcatgtcag---------------------------

upper sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 4
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag
|| || ||||||||||| || || || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||||| | | | | |  || | |    | | |       ||| |         ||  |      | |  |    ||  || || |                   
GCTGCCAGTTTTGGTGGGTCCAATATCGATCCTACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactggta-acatcatttgtcattacgttcattcctcatttccttttgattccttgctctgacgtttccttcaccatgttag-------------------

upper sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 4
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag
||| ||| |||||| ||  |||| || ||| | ||||| ||||| || ||||| |||||||| || ||||||||||| ||||||||     ||  || |     |   ||||           | || |   |||| |  | |||    | ||| | ||  | ||| |      |  |    |   
GCAACAACTTTTGGAGGTACTAATATTGATGCTACTGCTTGGGAAGACAAAAAGTGCAAAGGAGAGTCAAGGTTTCCGGCTCAGgtg---aaacttaaa-----tcacaatgactttcattgttttaagtctttattttgatatcttgtactaatataacttctttctcttaaattgtaacag---

upper sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 4
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag
||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||||||||| |||||||| |||||||||  | |  || ||  |  |  ||    |     | |||     ||  |  ||       | ||| | |   | |||||   |||   |  |   | |   
GCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAGgtaaaatatcattgatgaactgaaacacttaaattatcattctcaagactccct------tactgagtca--tagtatttcatttctcccaataaatag---

upper sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S168_104V6.1 (Physcomitrella patens), 5'ss of exon 4
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaatatagaat---attttgaaatggtgggagaccatgtatgagct-tatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag-----------------
|||||||||||||| ||||| |||||||| ||||| |||||||| || || |||||   ||| ||||| || ||||| |||||||| | |    | || ||     | | |||| |||    ||  | |   || |  |  | ||||| | |   || |||| |  ||  ||  || ||  |||    |                  
GCAGCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAGgttgaatctcaaagcattgcgatgttaaatagtgattcacggtttgccagatacaaatttaaat-agtaggtagaacatttgttaagtcactgcttatccactcaatttttatttgaccgtag

upper sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S4_323V6.1 (Physcomitrella patens), 5'ss of exon 3
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtag---tagaatatagaatattttgaaatggtgggagaccatgta---tgagctta---tctg-taaatcaatgaataaaacaatatttttgttccttctcttccttgtag
|||||||||||||| |||||||||||||||||||| |||||||| || || |||||    || || ||||| ||||| || ||||| |      ||   |  |  || |  |||  || |   |  |  |   | |  |||    ||| || | || |||   |  || |  |      |   ||| |  || |||
GCAGCAAGTTTTGGAGGCTCTAACATAGATCCAACCGCCTGGGAAGACAAGAAATGTCGGGGAGAGTCAAGATTTCCTGCCCAGgttggctctcaaaccacgacgttgttgaatattgtgtcgctgttcaagctaaatttaggtcctgctagaacactgaccgattcattgct--aacccgcactcatttttctag

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|24206077|gb|BU965330.1|BU965330
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|31459048|gb|CD401076.1|CD401076
EST:     GAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: GAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|208156515|gb|GD956825.1|GD956825
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATT
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATT
EST: gi|298190302|gb|HO032423.1|HO032423
EST:     CTGCCTGGGAGGATAAAAAATGCGAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGGAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|14011483|gb|BG726405.1|BG726405
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|6501903|gb|AW203276.1|AW203276
EST:     AAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: AAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|254341084|gb|GR854812.1|GR854812
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|4282613|gb|AI440553.1|AI440553
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGCGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|254320127|gb|GR831043.1|GR831043
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|192307583|gb|FG999622.1|FG999622
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTTTGCAAGGCATTGGAAGAAGATTTTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|13563366|gb|BG551595.1|BG551595
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|15000111|gb|BI320925.1|BI320925
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|208137092|gb|GD934536.1|GD934536
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGACAAAGGACAATTGGAAGAAGATT
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTG-CAA-GG-CA-TTGGAAGAAGATT
EST: gi|192320601|gb|FK012011.1|FK012011
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTTTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|31307475|gb|CD392678.1|CD392678
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|254336107|gb|GR841432.1|GR841432
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|192310236|gb|FK001934.1|FK001934
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|254336108|gb|GR841433.1|GR841433
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|22522815|gb|BU081626.1|BU081626
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|22522894|gb|BU081705.1|BU081705
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|9820747|gb|BE556257.1|BE556257
EST:     AGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: AGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|7232661|gb|AW568015.1|AW568015
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|4396720|gb|AI495717.1|AI495717
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG                         GTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
EST: gi|7232641|gb|AW567995.1|AW567995
EST:     CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAC                         GTAAGAATCCGTGTCAAGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC
genomic: CTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaat ... ttccttgtagGTAAGAATCCGTGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtagaatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag

- - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA