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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtgttgatttctacccagagcttgtggatttgatcattgctttctgaagtttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA

Basic information

species Glycine max
transcript GLYMA20G35760.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 10
gtaaagtgttgatttctacccagagcttgtggatttgatcattgctttctgaagtt----tttcccat-------gacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA
|||   |||| || |       |  | |||   ||||         |||   | |     ||||  ||       ||||||||||||||||||| |||||||||||  | |||||  |||||||| | |||||||| |||||||| ||| ||||| |||||||| |||||||||| ||||
gtatt-tgttaatgttcctgtggtacctgtaattttgcatgccatgttcaccaataaccatttcttattctttttgacagGATGCCATGTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTGACTGTATCAGCAGCACTGAAGCAAAAGA

upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
------------------------gtaaagt---gttgatttctacccagagcttgtggatttgatc------attgctttctgaagtttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA
                        ||||||     |   || |  |  |||   |     ||    |      | || |  ||| |  |||||  |   |||||||||||||| || |||||||||||  | |||||| |||||||  |||||||||| || ||||| ||| ||||| ||||||||||||||||||| ||||
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttc--aatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 10
------------------------gtaa--agtgttgatttctacccagagcttgtggatttg------atcattgctttctgaagtttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA
                        ||||  |    |  ||||  | || ||| ||| ||| |       | |||     | ||      ||  ||   ||||||||||||||||| ||||| |||||  | |||||| | |||||  |||||||||| |||||||| ||| ||||| ||||||||||||||||||| ||||
gaattacatggagcccaactacctgtaatgaacacttgtttcc-ctcaaagcatgtcgatgtttaggctaacataatggtatgtgtacattttcaatgcagGATGCCATGTCTGTTGCAAGAAACATTTTGAAAAATCCGAAACTCCTTCCTGGAGGTGGTGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

upper sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 9
gtaaagtgttgattt--ctacccagagcttgtggatttgatc-attgctttctgaagt----ttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA
|||     |||||||   |  |     | | | |||    || || |  |||||||||    |||||   | |||||||||||||||||| ||||| ||||| ||||| ||| |||| ||||||||||| || |||||||| ||||| ||| | ||||| || || || ||||| |
gtatctccttgatttaatttgctgttacatatagatcaactctatggagttctgaagtattgttttcttttaacagGATGCCATGTCTGTGGCAAGAAACATGATAAAGAATCCAAAGCTTGTTCCTGGTGGGGGTGCTACAGAGTTAACTGTTTCAGCTACCCTAAAACAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacccagagcttgtggatttgatcattgctttctgaagtttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA
                  atttgat  putative branch site (score: 5)
                                        tttttcccat  putative PPT
                                     aagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtgttgatttctacccagagcttgtggatttgatcattgctttctgaagtttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC