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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatgctccctatatatatatatatatatattcaaattcaattcattcttaaaagtggtaactgtttctggctttgatatcattctgtgtatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA

Basic information

species Glycine max
transcript GLYMA06G06850.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 5
gatatgctccctatatatatatatatatatattcaaattca-attcattcttaaaagtggtaactgtttctggctttgatatcattctgtgtatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA
                 |||  |  ||| |   |||    | |||  ||||      ||||   |  || ||   | |     | |   |   |  | ||||| |||||||| || || ||||| ||||||||||| |||||||||||||| ||||| 
----------------gtatg-acttatgtgaacaaggctacattacttctcttgcttggttgtttgttttgaactggtctctaattgcttgctgatacagGTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTG

upper sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 5
gatatgctccctatatatatatatatatatattcaaattcaattcattcttaaaagtggtaactgtttctggctttgat--atcat-tctgtgtatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA
               ||| | |  || |  |     |||   ||| | |||  |  |||||| |  |||||  || |     || | ||| | |    | ||||| |||||||| || ||||| || ||||| ||||| ||||| |||||||||||||| 
--------------gtatgtgt-catgtggacaaggatttg-ttcttcctttgatttggtaattagttctgaattggtctcgtcgtctctctttgatgtacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTG

upper sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 5
gatatgctccctatatatatatatatatatattcaaattcaattcattcttaaaagtggtaactgtttctggctttgatatcattctgtgtatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA
                     ||| |   | |   | |     | |   | |  |||   |||||  ||     |  ||    || ||  |    | ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||||||||| |||
--------------------gtatgttcttctctgactgttgcttaaaataatgagtcacaactgcatcaa---tgaattaatttttggcttctctacagGTTGATCCACTTACTCACCAAGTTAAGCTTTGTGACTTTGGAAGTGCAAAAGTGCTA

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|15815079|gb|BI787354.1|BI787354
EST:     CCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: CCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|12773946|gb|BG238873.1|BG238873
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|7283823|gb|AW596425.1|AW596425
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGAT
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGAT
EST: gi|5760433|gb|AI965724.1|AI965724
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|213600601|gb|DB960149.1|DB960149
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCATCTTACACACCAAGTGAAGCTATGTGAT
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGAT
EST: gi|208274892|gb|GE069728.1|GE069728
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|14990804|gb|BI316477.1|BI316477
EST:     CTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: CTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|193469053|gb|FK433705.1|FK433705
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|6455159|gb|AW185842.1|AW185842
EST:     ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|105634210|gb|DW247405.1|DW247405
EST:     ACACTGGTCCCAAAGTCTGCCACAGAGATTTGAAGCCTCAAAATATACTG                         GTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ACACTGGTCCCAAAGTTTGCCACAGAGATTTGAAGCCTCAAAATATACTGgtttgtttat ... tatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttaaaagtggtaactgtttctggctttgatatcattctgtgtatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA
                            tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatatgctccctatatatatatatatatatattcaaattcaattcattcttaaaagtggtaactgtttctggctttgatatcattctgtgtatattccagGTGGATCCTCTTACACACCAAGTGAAGCTATGTGATTTTGGAAGTGCAAAAGTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - tgctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg