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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggctcatttttaccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgcaagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA

Basic information

species Glycine max
transcript GLYMA08G22140.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
gtatgggctcatttttaccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgc----aagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
               |   || ||   |    ||||||||    ||      | |||| |||    | ||  |      |  | || | ||||| ||||||| ||||| ||  | ||||| || ||||| ||||||||||| ||||||||||| ||||| |||
--------------gttttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtttcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 10
gtatgggctcatttttaccctttttgtccgtg-taatatgtaagcaaaagtggaaacttgctttagtgacacatgcaag----tattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
               |   ||| ||  || || ||||||||    |||  || | |||| |||    | |   |  |      | ||   ||||| ||||||| ||||| ||  | ||||| |||| ||| ||||||||||| ||||||||||| ||||| |||
--------------gttttcttgttcaccatgctaatatgttga-aaacttgtatactttcttatacgtcttgtttactaacctgttccatttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 10
gtatgggctcatttttaccctttttgtccgtgtaatatgta---agcaaaagtggaaacttgctttagtgacacatgcaagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
        |    |||   |    ||    | | || |  |   || ||   ||  |    | ||   ||        || | ||   |||||||||| || ||||| ||  ||||||||||||| || ||||||||||| | ||||||||| ||||| |||
-------gttgcctttgttcaccatgctattatgatgtaaacttagtaagcttgttataaggtttctctgtggtccttaattgtttcattttttagATCGCAGATGGTGATCGGTTACCATTGGCCGTGAAGGAGTTGGGAAGCTGTGATCTTTATCCACAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgggctcatttttaccctttttgt-ccgtgtaatatgtaagcaaaagtggaaacttgctttag--tgac-acatgcaagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
|||   || |||  ||     | || | | |||  ||| |    |  |  ||     |   ||| |  |||  | | |    | || |||   |||| || |||||||||||||||| || |||  |||||| |||||||| ||||||||||| ||||| |||
gtacacgc-catacttgtaactcttatactgtggcataggatgacctatttgttttttgtttttcgcctgatgataagtttttgttctgtaacttagGTTACTGATGGAGAAAGGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgggctc-atttttaccctttttgtccgtgtaatatgtaagcaaaagtgg---aaacttgctttagtgacacatgcaagtattatgtttt------------ttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
|| | |   | | || || |  || | | | ||  ||  | || |    |||    |    |   || ||    | ||    | ||| | |||            ||||  | |||||||||||||  | || ||| ||||||| |||||||| ||||||||||| ||||| |||
gtctagctcctaattgtaactcttgtattc-tggcatgggaaaacctgcgtgactcagctatttatttgtactgcctgatgattttaagctttcatctctctaccttagGCTACTGATGGAGAAAGACTTCCCTTGTCTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 10
------gtatgggctcatttt-taccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgcaagtatt---atgtttttt-agATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
         |    |||  || | | | |||||      | | ||  ||||  |||||  || |  ||| ||   |||||     | ||   |||  || | || || ||||||||||||| || || ||||||||||||||||| || ||||||||||| || || |||
gtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatc-cttaaggttcacatttctttcttgccatgccttctcagGTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 10
----------gtatgggctcatttttaccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttag-------tgacacatgcaa----gtattatgt----tttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
           ||   |  ||  |||   ||||||| | | |    |||  |    |  |     |||  ||| |       | ||| |  |||    |||  || |    || | || || | ||||||||||| || || |||||||| || |||||||| |||||||| || |||||||||
gtttatttccctacatgtgcagatttcatctttttggctgagatggatgagaaactattttttctcttctttttgctttgtctaacatagtcaatttggtaacatctattattctcagGTTACAGATGGAGAAAGATTGCCTTTGGCTGTGAAAGAGTTGGGAACCTGTGACCTTTATCCTCAA

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|193660238|gb|FK603064.1|FK603064
EST:     ACTGTCAATATAAGGAGTGTAGGAGCAGACGTGGAG                         ATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGT
genomic: ACTGTCAATATAAGGAGTGTAGGAGCAGATGTGGAGgtatgggctc ... tgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGT
EST: gi|193334327|gb|FK297571.1|FK297571
EST:     AGTGTAGGAGCAGATGTGGAG                         ATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGT
genomic: AGTGTAGGAGCAGATGTGGAGgtatgggctc ... tgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagcaaaagtggaaacttgctttagtgacacatgcaagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA
                                             tgtttttt  CT-rich tract
                                     aagtattatgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgggctcatttttaccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgcaagtattatgttttttagATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG