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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG

Basic information

species Glycine max
transcript GLYMA10G41920.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 10
--aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG---------
  ||||| |    | |    || || ||||   |    |  |  | |||  | | ||    ||| |   |  |   ||  |       | |   |    ||||| |||||| |||||||| ||||| |||||||||||||||||||| |||||| | ||||| || || |||||||| ||| | || | |||          
ttaatttgttcagagaactttaaaatccttagctgcttcagttcatttg--ctttcatgggaacatgtgtactgataatgtctatatatatcttaacaacagGTTTGATGACACAAATCCAGAAGCCGAAAAGAAAGAGTATATTGACCACATTCAGGAAATCGTACACTGGATGGGATGGGAGCCCTACAAAGTTACATAT

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 10
----------------------aatttctgttaaaattcctataagcc--ttcattagaactttgtaattgaacatgcactataactttctttgttccaagttg--atggcttgtggc--acttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG---------
                       ||   |   ||    |||  ||| |  || ||| |  ||||        | ||| || |||      |      || | ||  |||  |  |  |  |    ||||| |||||||||||| ||||| || || |||||||| ||||| ||||||||| |||||||||| |  |||||||| ||| | || |  ||          
gtacgaaggaatagttagatgttatggttccaaaggagccttcaagtccattgatttgcccttttcttccttatatggac-atactgcattgcaaaacatgctgacatgattaatatctgaacaacagGTTTGATGATACAAACCCTGAGGCGGAGAAGAAAGAATATATAGATCACATTCAAGAAATTGTCCGATGGATGGGCTGGGAGCCTTATAAAGTTACCTAT

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 9
aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatg--cactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG---------
 ||| |||| | | ||    | ||  ||  ||      || |||   |   |     ||  | ||   |    ||    ||  | | || |   |    ||||| ||| || |||||||| ||||| ||||||||||| || || ||||||||| |||||||||| || |||||||| ||| |||| | |||          
-attgctgtgagacttgtgctcagttttgcttgatttgttttaaggcattgtaattgcttcagctga-tcaactcttttttttttgtttatttgaacaacagGTTTGACGACACAAATCCGGAAGCTGAAAAGAAAGAATACATAGATCACATTCAAGAAATTGTCCATTGGATGGGATGGGAACCCTACAAAGTAACATAC

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 10
-aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG---------
  ||| |||| | | ||    |  |  ||  ||      || |||   |   |  | |    |  |  || |||        | | || |   | |  ||| | |||||| |||||||| ||||| ||||||||||| || || ||||||||| | ||||| || || |||||||| ||| | || | |||          
acattgctgtgagacttgtggtttgttttgcttgatttgttttaagacattgta-attgcttcagttctttttctttaccatttgtttatttgaataacagATTTGATGACACAAATCCAGAAGCTGAAAAGAAAGAATACATAGATCACATTCAGGAAATCGTCCATTGGATGGGATGGGAGCCCTACAAAGTAACATAC

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
----------------aatttctgttaaaattcctataagccttcattagaactttgtaattga-acatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
                   || |  |  | || | |||   ||| |        |   |||       |   || |||    |  ||||| |  ||  | |    |     || ||||||||||||||||||||| || ||||||||| ||||||||||| |||| ||||||||||||||| |||||||||||||| |||| ||||||
gtaaaaaaagtttggttgcttttacttgagtttc-atacatctttacctttctataacaatccttgtttcttctgtaagca-caatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 10
aatttctg---ttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
  | | |    |||||| |   || | | | |||| ||| | ||    | ||   | |    || |||   |       |||  || ||| |  |||| | ||||||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| |||||||| | ||||||||||||| |||| ||||||
-gtctataaatttaaaagttgaatgaac-tccatttgaaatctgggcctaaattagtaaagaaattttaaattgcttttgtttgtgacttttc-cactgctagGTATGATGACACAAACCCTGAAGCTGAAAAGAAAGAATATATTGATCATATTGACGAAATTGTCCGGTGGATGGGTTGGGAACCTTTCAAG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 10
aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttg--ttccaagttga----tggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
    ||  || ||  || |  |   |||   |   ||     ||    | |    || ||| ||||| |   |||  |||| |    ||   ||||||  |   |||| ||| || ||||| || ||||| ||||||||||||||||||||||| ||||||||||| || || |||||||||||| |||| ||||||
----tcatttgaa--tcttggactgcttttcttccaccgaaaaaggataaagaagctttaagtttctatagtttctgagtttagttgtgctctgtggctatgttagGTTTGACGACACAAACCCAGAAGCTGAAAAGAAAGAGTATATTGATCATATTGAAGAAATCGTCCAATGGATGGGTTGGGAACCTTTCAAG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: EFJ20630 (Selaginella moellendorffii), 3'ss of exon 9
aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
                                                   |   |  | | || |  |    || |||  |   |  |  |     ||||| ||| ||||| ||||| || || |||||  |||| |||||||| |||||  |||| |||||  ||||||||||||||||||| ||||||
--------------------------------------------------gtaatcattgaattccactag--caggttcttatgtcttttctacggcagGTTTGACGATACGAATCCAGATGCCGAAAAAGAAGAATATATTGAACACATAAAAGAGATTGTAGAGTGGATGGGTTGGAAACCGTTCAAG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
lower sequence: EFJ32802 (Selaginella moellendorffii), 3'ss of exon 9
aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
                                                   |   |  | | || |  |    || |||  |   |  |  |     ||||| ||||||||| ||||| || || |||||  |||| |||||||| |||||  |||| |||||  ||||||||||||||||||| ||||||
--------------------------------------------------gtaatcattgaattccactag--caggttcttatgtcttttctacggcagGTTTGATGATACGAATCCAGATGCCGAAAAAGAAGAATATATTGAACACATAAAAGAGATTGTAGAGTGGATGGGTTGGAAACCGTTCAAG

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|208315330|gb|GE116150.1|GE116150
EST:     TTTATTGATTTTGGGTTGGCGAAAGACAGGGATGGAGGTTGCTATCTGAG                         GTATGATGATACAAATCCTGAAGCAGAAAAAGAAAGAGT
genomic: TTTATTGATTTTGGGCTGGCGAAAGACAGGGATGGAGGTTGCTATCTGAGgtgtgtactt ... gcacttccagGTATGATGATACAAATCCTGAAGCAGAAAA-GAAAGAGT
EST: gi|208147572|gb|GD945393.1|GD945393
EST:     TTTATTGATTTTGGGTTGGCGAAAGACAGGGATGGAGGTTGCTATCTGAG                         GTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACAT
genomic: TTTATTGATTTTGGGCTGGCGAAAGACAGGGATGGAGGTTGCTATCTGAGgtgtgtactt ... gcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
                                              cacttcc  CT-rich tract
           tataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttctgttaaaattcctataagccttcattagaactttgtaattgaacatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- -ttctgtt
- - - - - - - - - - - agccttc
- - - - - - - - - - - - - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggc