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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttggttcttgtgccagttacattacatgtcaagaattctaaattaatggaattgagatagctcggtttttaacttaatgacactgttgacatattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------------------------------cttggttcttgtgccagttacatt-acatgtcaagaattctaaattaatggaattgaga-tagctcggtttttaacttaatgacact--gttgacatatta-cagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC
                                                                                               |  |  |||    | ||  ||| |||| || |  |     ||||   |  || || | | |   | |||   | ||  |||      |||   | |||  |||| ||||| ||  |||| ||| | ||||| | ||| ||||| ||| |||| | ||| ||||||||||||||||| ||||||||| | |||||||| |||||
gtgagttctctctctctgattattttcgataatttcttagattttctgtttctagcatatagaagaaagatgtgtaatttgaatctttagggcagttatggttgactgaatttgattcacatttccattagaacgaattggggagatggaaagttgaaagctttaggagtttttgaattctggtttttaaattggcagAGATACAAGCTACTGGAAGTTCATATGGGACTCATTTTCGAGTTTCAACTTTTGGAGAATCACATGGAGGAGGAGTTGGTTGTATCATTGATGGTTGTCC

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------------------------------------------cttggttcttgtgccagttacattacatgtcaagaattc--taaattaatggaattgagatagctcggtttttaacttaatgacactgt---tgacatatta-----cagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC
                                                                  ||   | | | | |   | |  || ||| |  |   |||  |   | ||    ||| ||| |  |   || | ||       || |||    | ||| | |      ||||  | |||||  | || | |||||  ||||   ||||||||||||||||||| || ||||| | ||| || |||||||||||  ||||||||||||||||
gtgagtttctttccatttccattcaccacccaaatctctccaatattacgattttggcttgtgaatctgtttcccttttcttttcagttttcatctttaacgttccctgcctgaaccacatttagaaa--ttaattctaaagcagtaaaccctgaatgttacaaaatgaaaaccagAAGTGCAGGCCTCAGGAAATACCTTAGGAACATACTTTCGTGTTACAACATACGGAGAATCTCGTGGTGGCGGTGTTGGTTGCATTATTGATGGATGTCC

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 1
cttggttcttgtgccagttacattacatgtcaagaattctaaattaatggaattgagatagctcggtttttaacttaatgacactg-ttgacatattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC
  |  ||   |    |  |    ||    |     |||||      ||| | |||  | |  ||    || ||||     |   || |||    || ||||| |||||||| ||||||||||| |||||||   | || |||||||| |||||||| ||||| |||||||| |||||||||||  | ||||||||||||||
tgtaatttaaggataaaattttctatgctttctctattcttttgatatgaagttgcaa-acttcaaacttcaactctgacatcttgcttgctgaataacagAAATACAGGCAGCTGGGAGTACATATGGAACATATTTCCGTGTTACGACATATGGAGAATCTCATGGAGGTGGTGTTGGTTGCATAATTGATGGATGTCC

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|37994824|gb|CF806413.1|CF806413
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         GCATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|209717805|gb|BW668942.1|BW668942
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|14125803|gb|BG790241.1|BG790241
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAATAGACTTC                         GCATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|254322919|gb|GR835634.1|GR835634
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|213594424|gb|DB970018.1|DB970018
EST:     CCCCGCCTACCTACGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTAC
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTAC
EST: gi|37996436|gb|CF808025.1|CF808025
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         GCATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|254316986|gb|GR828523.1|GR828523
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|10709332|gb|BF009056.1|BF009056
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCCGGTTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACA
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGC-GGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACA
EST: gi|192325343|gb|FK017144.1|FK017144
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|298181206|gb|HO022645.1|HO022645
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         GCATACAGGCGGCTAGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|192296954|gb|FG991950.1|FG991950
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|254340228|gb|GR858353.1|GR858353
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|298168931|gb|HO009861.1|HO009861
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         GCATACAGTGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACA
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAG-GCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACA
EST: gi|7692116|gb|AW760231.1|AW760231
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|209706545|gb|BW667810.1|BW667810
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|213594292|gb|DB969970.1|DB969970
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         ACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
EST: gi|21286048|gb|BQ473919.1|BQ473919
EST:     CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTC                         GCATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT
genomic: CCCCGCCTACCTCCGACTCTCACTCCGTCCTCGTCTTCCCAAGAGACTTCgttagtcctc ... catattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggaattgagatagctcggtttttaacttaatgacactgttgacatattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC
                     tttttaacttaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttggttcttgtgccagttacattacatgtcaagaattctaaattaatggaattgagatagctcggtttttaacttaatgacactgttgacatattacagACATACAGGCGGCTGGGAGTACCTATGGAAATCACTTTCGTGTTACAACATATGGGGAATCACATGGAGGAGGTGTTGGTTGTGTTATTGATGGATGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - -cttgtgc
- - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg