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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG

Basic information

species Glycine max
transcript GLYMA07G40300.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 18
cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggat-tctcata-acaatttct-------ccatgttgcaaaaatcgtccgt--agGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
             ||  ||| ||  ||| ||| |    |  | | ||||   ||| | || | ||| | |||| || |       |  ||   |||  |   ||| |  |||||||||||||| | || ||||| ||||| ||||| || ||  | ||||||||||||||||| ||||||||||| || |||||| | |||||  | || |
---------ctcatatcaacctgttccactttccca--cggccatgattattttttgaatgtgtcaaacacaaattttgaattgcctgtgacacaattactctcccttaagGATACGATGGCCCGGAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
cttttttagaaggtacaaacatgaaccaat-ttacagtccatctagg--attcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
 | ||    ||| ||  ||||||    | | ||   ||     |  |  | | |||| |   ||  | |  |||||      || | |    |   | |  ||||||| |||||  | | |||||| ||||| ||||| || || ||||||||||| || ||||| |||||||||||||| |||||| | || || || || |
atgttccttaagata--aacatgttgtattgttgttgttggcatgagttacttacttccat-ttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 3'ss of exon 18
---------------------cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgt----agGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
                      || || | || || ||      ||  | |||  |   |||||    |  |   | | |       |  | | | ||  | ||| ||   |   |  |    |||| ||||||   ||||| || | |||||| || || ||||| | |||||| ||||||||||| ||||| ||||| ||||||||||| | ||| || || |
gtaagtcagaatccttcttttattcttcaaaaagttcatcgtgaaaagattttgaaaatcatct----tctagagtagaaaggattaattagtatatcgtttttgtaatcctttcctattttcagGACACGATGCTTAGAAAGCCAGTAGATCCTGAGGAAGAGCTTAAATGGATATCTCAAGAAGTCCGTGGGTATGTGGAAGCTGTTCTCAGCAGTCTTGCGG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgt---agGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
 |||| |   |  || |  |   | |   ||| || |  |    | || ||    |    || | ||      ||| |||  | |||   |  || ||   ||||||| |||||  | |  ||||| ||||| ||||| || ||  ||||||||||||||||||| ||||||||||||||||||||| | |||||  | ||||
-ttttatcttacctaaaggctaaagcatgttttcatttaaat--gtatccaaacacaagatcacttattttactcttcattctacaactcttttctgtttaagGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------cttttttagaaggtacaaacatgaa---ccaatttac--agtccatctaggattc------------actttcggattctcata-acaatttctccatgttg-caaaaatcgtccgta-gGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
                                                                             |  ||||  ||| |  | |||| |    ||  || |   ||   | | ||||              |||     |||   ||| ||||  |   ||| |   || | |   | || | |||| | |||||  | | ||| || ||||| ||||| || || |||||||||||||||||||| |||||||||||||| |||||| | || || || || |
gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaatactgctccattaaaatacacaaactaaacatctgatcatacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
--------------------------------------------------------------------cttttttagaaggtacaaa----catgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccat---gttgcaaaaatcg-------------------tccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
                                                                    ||   | |  |  ||  ||    ||| |   |||||   ||||   |     |       |       ||||  |||| |||||     | || |||                      ||   ||||||| |||||  | | |||||| ||||| ||||| || || |||||||||||||||||||| ||||||||||| || |||||| | || || || || |
gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 18
-cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
 ||  |||  ||  |  | | | |      || ||| |  |  |     |   ||      | |  | | | || |    | || |     |       |||||| |||||  || |||||    |||||||||||||||||| | |||||||| |||||||| || ||||| ||||||||||||||||||||||| || |
actacttttaaacttg-acataagttatgtttgacatttaaggtttttattgtttataatattttctgagacttacgtttttttccttgtctgtatttcagGATAAGATGGTTAGGAAACCCATCGATCCAGAAGAGGAGCTCCGGTGGATGTCCCAAGAAGTACGGGGTTACGTTGAAGCTGTTCTTAACAGCCTTGCAG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatg-ttgcaaaaat------cgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
        |     | |    ||        |      | | |||| |||    | ||  |   || ||| |||  || || |||   || |      | |    |||||| |||||  || ||||| |  || || ||||||||  |  | |||||||| |||||||| || |||||||||||||||||||| ||||| || ||||
-----agggttaagatagctttgtttgggcatgtgaggcgtttaggtttccggatggg--tggtattacagttttgccttggttgtctaatttttttcctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG

upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 18
cttttttagaaggtaca-aacatgaaccaatttacagtcca---tctaggattcactttcggat-tctcataacaatttctccat-gttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
 || | ||   |   || ||||| ||    | || ||| ||   | |   |||   | |  | | | |  |    | |  |   | |     |||||  |   |||||||| |||||||||| |||||| ||||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||
-ttctgtactggccccagaacataaat---tctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggttgccttgaaaat--tttatagGATACAATGGCCAGAAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTG

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|17518741|gb|BM187783.1|BM187783
EST:     TTGGTGAACCTAGTTTTCCTATGCGACAAAGCCTTTCTGATGGTTCTCTT                         GATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATG
genomic: TTGGTGAACCTAGTTTTCCTATGCGACAAAGCCTTTCTGATGGTTCTCTTgtaagtttct ... tcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATG
EST: gi|13252141|gb|BG363044.1|BG363044
EST:     TTGGTGAACCTAGTTTTCCTATGCGACAAAGCCTTTCTGATGGTTCTCTT                         GATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATG
genomic: TTGGTGAACCTAGTTTTCCTATGCGACAAAGCCTTTCTGATGGTTCTCTTgtaagtttct ... tcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG
                 tcataac  putative branch site (score: 2)
                   ataacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttttagaaggtacaaacatgaaccaatttacagtccatctaggattcactttcggattctcataacaatttctccatgttgcaaaaatcgtccgtagGATACGATGGCCAGAAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - -ccatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt