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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaatatacatctgaatatttttggaaagtggaaatacttagcactttgactgaacataaccaaagttaatgttcactttttgtttggttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT

Basic information

species Glycine max
transcript GLYMA15G07480.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
gttcgaatatacatctgaatatttttggaaagtggaaatacttagcact-ttgactgaacataaccaaagttaatgttcactttttgtttggttgc-----atacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATA-AATTACTTTGT
         ||    |   |  || | | ||    |  | |   ||| |  || ||  |  |   |   |   |||| || | |    ||||  |      || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |  ||||| ||  | || || |||||    ||  | ||||| |  | ||| | 
------ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgt-cattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG-

upper sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------gttcgaatatacatct---gaatatttt----tggaaagtggaaatacttagcactttgactgaacataaccaa--agttaatgttcac--tttttgtttggttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT
                                                                                      |    | |||  | |   |||  | ||    |  |||  ||| | | |  |   ||       | ||   |||  |||  || |   |  ||||    |   || || |||||||| || ||||||||||| || ||||| || ||||||||||||||||  || ||  | || || || ||| |||  ||  | | || |        | 
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA

upper sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
-gttcgaatatacatctgaatatttttggaaagtggaaatacttagcactttgactgaacataaccaaagttaatgttcactttttgtttggttg-catacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT
 | |  || |||    || | ||| ||  | |        | |     ||| | |  |   | |    || | |||  || |  ||| |   |   ||| ||||||||||| |||||||||||||| ||||| || || || |||||||| |  ||||| ||| | || ||  ||||    ||| | |||| ||  |     |
aggttcaacata-gcatggacattcttacatac--atttcaatcgtttcttagtcaaattttcattttagatcatgaccattgattgctcactcaacatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT

upper sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gttcgaatatacatctgaatatttttggaaagtggaaatacttagcactttgactgaacataaccaaagttaatgttcactttttgtttggttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT-
                |    ||||     |       | || |      |||   ||| | |         |  |   |  ||| || |   || | |||||||| || |||||||||||||| ||||| |||||||| ||||||||||  || ||  | || || |||||||| |  ||| | | |    |    | || 
----------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagcccttt-ttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAA-GTGTGGTGTGGTA

upper sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------gttcgaatatacatctgaa------tatttttggaaagtggaa-ata------cttagcactttgactgaacataaccaaagttaatgtt---cactttttgtttgg-ttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT
                                              ||  | |||| |||  | |      | ||| ||     || |  |||      |||     ||  | |   |   |  | || |  | |     | | ||  | ||   |   | ||||||||||| |||||||||||||| ||||| || ||||| ||||||||||  ||||| ||  | || || |||||| ||||  | ||||| |      |  
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

upper sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
gttcgaatatacatctgaatatttttggaaagtggaaa---tacttagcactttgactgaacataaccaa--agttaatgttcactttttgtttggttgca-------tacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT
|| | | |   | |    ||   |    |    |||||   ||  || | ||   | |      || ||   || |  |||||||| ||| | | ||| ||       | ||||||||||||||||||||||| |||||||| || || |||||||||||||  || || ||||||||||| ||||||| |||| | | |      | ||   
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

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|6846844|gb|AW349134.1|AW349134
EST:     GATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAG                         CAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAG
genomic: GATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAGgttcgaatat ... ttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAG
EST: gi|14991403|gb|BI317076.1|BI317076
EST:     GATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAG                         CAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAG
genomic: GATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAGgttcgaatat ... ttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAG
EST: gi|4284462|gb|AI440784.1|AI440784
EST:     GATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAG                         CAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAG
genomic: GATTTGGATTGTTCTGCATTGAAACATTGATCAGTATCTGGGTTATTCAGgttcgaatat ... ttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttgactgaacataaccaaagttaatgttcactttttgtttggttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT
                   aaagttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaatatacatctgaatatttttggaaagtggaaatacttagcactttgactgaacataaccaaagttaatgttcactttttgtttggttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA