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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG

Basic information

species Glycine max
transcript GLYMA06G32680.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 5
-atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
 ||||||   ||| |  || |  |   |   ||  ||   |  |  ||      ||||  | |     ||  |   | |  ||| |||    |  |  ||||||||||||||||| |||||||| ||||| || |||||||||||||| ||| ||||| ||||||| ||||| || || |||||||| ||  | || || |
gatatttagtgtt-gaggtgatctaattagtctatatttgtttacatacagaaatgttactaagtccatctatgaactccatttctttgccaatataacagGAACAACAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCTGCTGCATTTGGTGGAGTGTGCATTG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 5
atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttg-tttattaaattttcggttgtca-ctttttttttttttaattt--gcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
   | | ||  | || |  | ||| |         ||    |||    ||| ||| |||| | ||    |   | | | ||   ||| | | | | |    |||||||| |||||||| |||||||| ||||| || |||||||||||||| ||| ||||| ||||||| ||||| || || |||||||| ||  | || || |
---tctatatatagtgg-gatatttagtgttgaggtgatctaatagtctatattggtttactcaaaggccatctataaactccatttctatgtcactataacagGAACAGCAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCCGCTGCATTTGGTGGAGTGTGCATTG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 6
atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatg-----ttgtttattaaattttcggttgtcactttttttttttttaatttg-cagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
      |||   |  |  || | |  |    || ||  |||  |||   |||     || |     ||    |   ||   ||        |||  |||||  ||||| ||||||||||| ||||| || ||||| || || || || ||||||||| ||||| ||||||| || || || || |||||||| ||  | || || |
------gtaaaataaaacaaaactatt---ttctatatctgg-tctggaatgcagaattatcatgcaagagctacctttaaaccaccaacctttgcaatttaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCGAATTTACAGAAAGAATTGAACAGATACATCCCTACAGCTGCTGCATTTGGTGGAGTCTGCATTG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
--atatttgtagtt--tgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
  |  | |  || |  |||  ||   ||      || | |     ||   | ||||      ||||    |  | |  || || |     |   || | ||||||||||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||||||||| ||||| || || |||||||| ||  |||| ||||
taacgtgttgagctactgttttatatttggctcactaattatgcaaactcactatgcaaca-atta--cctgtgatcatc-ctctgacactggatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 5
-atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
 | | |  || | |  |  |   ||||   ||  |     ||||  | |  | | |   | |    |  |   ||   ||     |   | | || ||||||||||||||||||| ||||| || ||||| || || ||||||||||| ||||| ||||||||||| ||||| || || |||||||| ||  |||| || |
tacaat-ataatcttaatgatttttcacatgcctatcagttgaagatttggtatggagcagtttgctaacctgtgatcctgacactggatattatatgcagGAACAACAAATGGTGATGCCAGGCCATCGTGAGTCGAACTTGCAGAAGGAACTTAACCGATACATCCCCACTGCTGCTGCATTTGGTGGTGTATGCATTG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 6
------atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
        | |  | || | || || |   |||    |  |      |   |   ||| |  |   | |  |||   ||   ||  ||    |    | |   ||||| ||||||||||| ||||| || ||||| || |||||| |||| |  ||||||||| ||||||| || || || ||||||||||||||  | || || |
ggagttggactactggtgt-taatagggc-catagttttcacatgcaagatttccatgctagtg--tgagcttt--atttaaacccttaccctggcaattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAACTGAACAGATACATCCCAACTGCTGCAGCATTTGGAGGAGTGTGCATTG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttat-taaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
                    || |||  |  ||     || |   | ||         |   |||||||| |||      |  || |||   ||  |||   |   ||||   ||  ||||||||||||||| | |||||||| || || ||||| ||| | ||||  ||| ||||||| ||||||||||| || || || |||||||| || ||||| |
gtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactga-actcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ11193 (Selaginella moellendorffii), 3'ss of exon 5
atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
                                  | ||  |||  | |||  | ||   |  |  ||||     | |||| | |       |||| |||||| ||||||||||| ||||| ||||| || ||| | ||| | ||||  ||||| || || |||||||| |||||||| || ||||| || || |||||||
--------------------------------gtaagcaagaactt-ttagctcgtaactcgatctttc-----tgacttctctccccgggaatt-gcagGAGCAACAAATGGTCATGCCCGGACACCGAGAAGCCAACCTCCAGAGGGAACTCAATCGCTACATTCCAACCGCGGCGGCCTTTGGTGGTATTTGTATCG

upper sequence: GLYMA06G32680.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 5
atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
                                         || | |  |  ||   |  ||| |      ||      || | |       | |||||||| ||||||||||| ||||| ||||| || ||| | ||| | ||||  ||||| || || |||||||| |||||||| || ||||| || || |||||||
---------------------------------------gtaagcaagaactttagctcgtaactcgatcttttctgacttctctccccgggaattgcagGAGCAACAAATGGTGATGCCCGGACACCGAGAAGCCAACCTCCAGAGGGAACTCAATCGCTACATTCCAACCGCGGCCGCCTTTGGTGGTATTTGTATCG

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|21889820|gb|BQ743033.1|BQ743033
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|10255666|gb|BE823432.1|BE823432
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|37997748|gb|CF809337.1|CF809337
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|16345250|gb|BI970845.1|BI970845
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|254316637|gb|GR828174.1|GR828174
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|254327677|gb|GR834642.1|GR834642
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|207831944|gb|GD803846.1|GD803846
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|254329867|gb|GR839420.1|GR839420
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|7041896|gb|AW471790.1|AW471790
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|192309135|gb|FG999404.1|FG999404
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|6228042|gb|AW156641.1|AW156641
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|37995033|gb|CF806622.1|CF806622
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
EST: gi|7234480|gb|AW569817.1|AW569817
EST:     GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAG                         GAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA
genomic: GGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgacta ... taatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG
                                          ttttaat  putative branch site (score: 3)
                   ttttcggttgtcactt  CT-rich tract
                          ttgtcacttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttgtagtttgtagtaagattcatgagctcaatgcctgaatctattatgttgtttattaaattttcggttgtcactttttttttttttaatttgcagGAACAACAAATGGTAATGCCTGGACATCGGGAATCAAACTTGCAGAAAGAACTGAACCGATACATTCCCACCGCGGCAGCATTTGGAGGCATATGTATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG