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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

Basic information

species Glycine max
transcript GLYMA14G36540.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G097226_T01 (Zea mays), 3'ss of exon 11
------------------gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC
                  || | |||||   || |   | |    |  |   |||| | | |    ||| ||   || | || |  ||  | || ||  |      | |||| || ||  | || |||||| | || |||||| || |  | || ||||| |||||||||||||||||| |  ||||||| |||||||||||||| || |
gtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccata-tgccatctgtagtaccttacttttggttcatatttgttg----acagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 5
------------------gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC
                  || | | |||   || |   | |    |  |  |||||    | |   ||| ||    | | || |  ||  | || ||  |      | |||| || ||  | || || ||| | || |||||| || |  | || ||||| ||||| |||||||||||| |  ||||||| |||||||||||||| ||||
gtaattcattttgtagacgttatagtttcacttgttcagtatggccatctacttttctccatatgccatctgtagcaccttacttttggttcatatttgttg----acagGTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTTAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCTC

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC
     |      ||| ||     || ||         |||  |||  | ||  | |   ||  ||   |      ||||   ||  || ||||| || ||| | || |||||||| |||||||| ||| |||| ||||||||||| || |||||||| |  ||  |||| |||||||||||||| || || |
---gtatgaagatttttagatttctctcttgtaaacctgcttaaatctgatacgtgaactctgaacttttttctttgttaaaat--gcttagGTAATAAATCTTCGATCAATCCGTCCGCTTGACCGAGCCACCATCAATGCTTCAGTGAGGAAAACGAGTAGATTGGTAACAGTTGAAGAAGGTTTCCCAC

upper sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 3'ss of exon 11
------------------gtaaaactttagtttataatgaactttccccctc-----ttttg------caaaaa----cttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC
                  | ||   |||  ||| || || | |    |         |||||      || |||     | ||||  | || | |  |  |  | || ||||||  |    | |||| || ||| | || |||||||| || |||||  ||||  ||||||||||||| ||||||||||| | ||| |||||||| |||||||| ||||| ||||
gtaactcaaaagaagtttgaaattattttctttgtattggattcagacaactagtagttttggaagttcagaaaggtattccattcagtttttaaggaaagcaattgttgttctgtttgatacagGTTATAAATCTTCGCTCAATCCGTCCCCTTGACAGATCGGCAATCAATGCTTCAGTCAGGAAAACTAGCAGACTGGTGACTGTTGAAGAGGGGTTCCCTC

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|120495804|gb|EH223971.1|EH223971
EST:     AGGAAGGAATCAGTGCTGAG                         TTCATTAATTTGCGTTCAATCCGGCCGCTTTGATCGATCCACAATCAATGC
genomic: AGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGC-TTGATCGATCCACAATCAATGC
EST: gi|254335255|gb|GR846752.1|GR846752
EST:     GCTGCCTGAGACACTGGCAAAGGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTG-CTGAGACACTGGCAAA-GGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|20498733|gb|BQ273663.1|BQ273663
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|254319589|gb|GR829101.1|GR829101
EST:     GCTGCTGAGACACTGGCAAAGG-AGGGATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|20498857|gb|BQ273787.1|BQ273787
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGACCGCTTGATCGGTCCACAAT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAAT
EST: gi|19053203|gb|BM731870.1|BM731870
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|9439950|gb|BE440462.1|BE440462
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|37994649|gb|CF806308.1|CF806308
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|298169681|gb|HO021041.1|HO021041
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|17962851|gb|BM269607.1|BM269607
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|5606648|gb|AI900746.1|AI900746
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|254334369|gb|GR844154.1|GR844154
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|254335254|gb|GR846751.1|GR846751
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         -TCATTAATTTGCGGTCAATCCGGC-GCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|11412033|gb|BF424044.1|BF424044
EST:     GCTGCTGAGACACT-GCAAAAGGAA-GAATCAGNTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGC
genomic: GCTGCTGAGACACTGGC-AAAGGAAGGAATCAG-TGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGC
EST: gi|10845821|gb|BF068863.1|BF068863
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|9565969|gb|BE475478.1|BE475478
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|151397384|gb|EV267257.1|EV267257
EST:     GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
EST: gi|6848027|gb|AW350317.1|AW350317
EST:     GCTGCTGAGACACTNNCAAANNNAGGAATCAGTGCTGAG                         GTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT
genomic: GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacttt ... atccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC
                                        ttcttatcc  CT-rich tract
                   ttatcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatagGTCATTAATTTGCGTTCAATCCGGCCGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG