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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattttattttatcaggaaacatgtttccatgttgtattagtattttgttgttttattcatggacctgtgtcatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCCG

Basic information

species Glycine max
transcript GLYMA04G39390.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
ttattttattttatcaggaaacatg-tttccatgttgtattagtattttgttgttttattcatggacctgtgtcatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCCG
| ||    |||  |         |  |||  ||  ||| |  | |||   || | || ||  |       |||  |||     | ||   |    |||||||| || |||||||| || ||||||||  ||||||| || || ||||| || || ||| |||| || ||||||||||||||||| || ||||| |  || |
tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgttttcacttt-taattcattgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
















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|208316033|gb|GE111001.1|GE111001
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|13312215|gb|BG405796.1|BG405796
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|17401015|gb|BM177797.1|BM177797
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|31460812|gb|CD402840.1|CD402840
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|9203484|gb|BE329708.1|BE329708
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|208246050|gb|GE045664.1|GE045664
EST:     GTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: GTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|193516138|gb|FK473820.1|FK473820
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGC
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGC
EST: gi|209726920|gb|BW680262.1|BW680262
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|207763084|gb|GD731215.1|GD731215
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|151406465|gb|EV276280.1|EV276280
EST:     ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: ATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
EST: gi|15000708|gb|BI321522.1|BI321522
EST:     CCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAG                         AACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT
genomic: CCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaac ... aaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgttttattcatggacctgtgtcatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCCG
                                       atatgtaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattttattttatcaggaaacatgtttccatgttgtattagtattttgttgttttattcatggacctgtgtcatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - -catgttt
- - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagtg