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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgagccacgcggttgggttgaattgcagttattcctttttatttattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC

Basic information

species Glycine max
transcript GLYMA06G02100.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g58650.1 (Oryza sativa), 3'ss of exon 3
-----------------------gttgagccacgcggttgggttgaattgcagttattcctttttatttatttt--gctccatgcatct-tacat------------atctcaggggaatcatttggctttttatt------agGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
                       ||   | | |  | ||   ||| || ||| ||||  | |  || | ||| |  || | || ||| | ||||             ||          | ||||  ||||||  |      |||| |||||||| || || ||||| ||||||||  |  ||||||| ||||||||||||| ||||||||| || ||| ||||||||||| | |||||||| |
gtaatgggatatcatatgttcaggtcttgacgccggtttttcttgtatggca-ttatgtcatactactaattattagcacaattcatttgtacacttgagccatgaaattgtgacatgtttatttacctttttcatcgacacagGTTGCTGAAAATCTAGCTCAGCTTATGTACAGTGTTCTGATGACCGGATACATGTTCAGGAATGCGCAGTATCGTCTGGAATTGCAACAGAGTTTGGAGC

upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G140809_T01 (Zea mays), 3'ss of exon 3
--gttgag------ccacgcggttgggttgaattgcagttattcctttttatttattttgctccatgcatcttaca-----tatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
   |||||      | |  |   ||| |    |  || |      |||  ||||    ||     ||  ||||        |   |       || || |    |   |  |||| |||||||| || || ||||| ||||||||  || | ||||||||||||||||| | |||||| || |||||| ||||| ||||| | |||||||| |
gtattgagtacctcctattcctatggctgttttcccaatggaaaatttacattttgcatgacatttgtgtcttttgattgttgctttgttacgattatcttttatcaaaacagGTCGCTGAAAATCTGGCTCAGCTTATGTACAGTGTCCTAATGACTGGATACATGTTTAGGAATGCACAGTACCGTCTGGAACTGCAACAGAGTTTGGAGC

upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
---gttgagccacgcggttgggttgaattgcagttattcctttttatttattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
     ||    | |     |  |    || ||   | |  | | || |   |||| | | || || |   || | |       | ||||     ||   |||||| ||||| |||||||||||||| |||   ||| |  ||||||||||||| ||||| |  || || ||||| ||| | ||||||||| |||||||||| |
gtgagtgctttatgtaagcga-tacgttttcaacaagt--tgtgtactgtgtttgttacttggattt---atttgttgaattgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC

upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g00090.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------gttgagccacgc-ggttgggtt--gaattgcagttattcctttttatttattttg------ctccatgcatcttacatatctcagg--ggaatcatttggctttttatt-agGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
                                                |||   | || |||| | ||  |  ||    || ||  | || || |  | |        ||||  |  | |  || |   |    ||||||| |||| |||   || |||| |||||||| ||||| ||||||||||||||  | |||||||||||||| ||||| |||||||| |||||  | |||||| ||||| |||||||||| |
gtaagtttgttactatctcatgaacatggatttcagaggagttataagtgattaatgccggtttgtttttgtgttcatattttttgtattaatctgatgtaatgggtttccaacctccatgtatgttataatctggaatcacttggttttcctttcagGTTGCTGAAAATCTTGCCCAGCTCATGTACAGTGTTATGATGACTGGATATATGTTTAAGAATGCTCAATATAGGTTGGAACTGCAACAAAGTTTGGAGC

upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S207_10V6.1 (Physcomitrella patens), 3'ss of exon 4
gttgagccacgcggttgggttgaattgcagtt--attcctttttatttattttgctccatgcatcttacatatctcagggga-----atcatttggctttttat-tagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
            |||  |  ||||  ||||||  || |    | |  |    || |   |  ||||   |  |  |||| |       |  ||||     || |  || ||||||| ||||| || ||||||||||||||| | |||||||||||||||||||||| ||| || || || ||  | ||||||||| | || |||   |
-------tgtatggtaagcctgaagagcagttttatacgccgtcacatggagtgttagcttaatctggtac-taacaggagtttactgtattttgaaacattgtgcagATAGCTGAGAACCTAGCGCAGCTCATGTACAGCGTGATGATGACTGGATACATGTTCAGGAACGCTCAGTATCGACTAGAATTGCAACAGAGCTTGAGCC

upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_187V6.2 (Physcomitrella patens), 3'ss of exon 3
--gttgagccacgcg-gttgggttgaattgcagttattcctttttatttattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
  |   ||  | ||   ||   |  | |  ||  |   | |         | ||| |   ||  ||| | |    |  |  |  | |     || |  |   | |||| || || || || ||||||||||||||| | |||||||||||||||||||||| |||||| || || ||  | ||||||||  | || ||| | |
atggcaaggtatgcacattaaatctagtcacatatgcacatgcacgaagctgttgttttctggttctaagaggagtttgctgggttacaatactctgca---gATAGCCGAGAATCTGGCGCAGCTCATGTACAGCGTGATGATGACTGGATACATGTTCAGGAATGCCCAGTATCGACTAGAATTGCAGCAGAGCTTGAACC

upper sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ23149 (Selaginella moellendorffii), 3'ss of exon 3
gttgagccacgcggttgggttgaattgcagttattcctttttatttattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
                                         || |  ||||  |   |   || | | |  |   |   || || |||   ||||  ||||| ||||| || ||||| ||||||||||| ||| || | ||||| ||||| ||||| |  ||||||||||||||| | || |||||| ||||| | ||||
----------------------------------------gtaatggttttagtttgttggtccttctt--cgtggttaaaacacttgtgctttt-ctagGTGGCTGAGAATCTTGCTCAGCTCATGTATAGCGTCCTAATGACAGGATATATGTTTAGAAATGCGCAATACCGTCTCGAGTTGCAACAAAGTCTAGAAC

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|7926546|gb|AW832572.1|AW832572
EST:     ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|13481313|gb|BG510656.1|BG510656
EST:     ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|151400265|gb|EV270079.1|EV270079
EST:     GCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: GCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|58022494|gb|CX709235.1|CX709235
EST:     CCCCTCAA-TTTTTGCTGTAACAATTACCACT                         GTAGCTGAAACCCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: CCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|213604870|gb|DB956155.1|DB956155
EST:     ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|192306875|gb|FK003045.1|FK003045
EST:     ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|58015936|gb|CX702678.1|CX702678
EST:     GCTGTAACAATTACCCCG                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: GCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|6718506|gb|AW306153.1|AW306153
EST:     ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|10709507|gb|BF009231.1|BF009231
EST:     ATATGATTGGAACACTGCCCNCTCAATTNTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
EST: gi|57574786|gb|CX547761.1|CX547761
EST:     TATGATTGGAACACTGCCCCCTCAAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACC-TGCACNAGCTCATGTACAGCATCATGATGACTGGATA
genomic: TATGATTGGAACACTGCCCCCTC-AATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCAC-AGCTCATGTACAGCATCATGATGACTGGATA
EST: gi|11687314|gb|BF594954.1|BF594954
EST:     ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACT                         GTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC
genomic: ATATGATTGGAACACTGCCCCCTCAATTTTTTGCTGTAACAATTACCACTgtaagatgtt ... tttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
               atcttac  putative branch site (score: 3)
                                            ctttttatt  putative PPT
                                             tttttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgagccacgcggttgggttgaattgcagttattcctttttatttattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - agccacg
- - - - - - ggttggg
- - - - - - - - - - - - -tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatct