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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG

Basic information

species Glycine max
transcript GLYMA01G00870.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 6
gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
             | | |||| | ||   ||   | |||   | |||  |     ||  |||   |||| | |||  ||  | |    |   ||||   | |||| || || ||||| ||||| ||||||||||| || |||||||||||  | || || ||||| || |||||||| ||||| |||| ||| |||||||| |
------------gtactttcttctttccagc---acacttg-agtttggattttctt--cat-gctaatcgctaagattgatgttgaattgtttgc---acagGTGATCGACAAGTCCTTTGGTTTTGACACTGCGGTGGAGGAGGCTCAGAGGGCCATCAATGCTGCTCATGTTGAGGCTGAGAGTGCAGAGAATGGCATTG

upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 8
gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
|||| |  | ||||||    || ||||   | |||   | || | |||      ||  |||| |||  ||           ||| |  | | |        |||| ||||| |  || ||||| || |||||||| ||||||||||| ||||| || |||||||| || ||||| ||||||| ||| |  || ||||| ||||
gtaa-tgatctttttcacattatattg--acattagggt-atgaattatggtgtatatgcataatttgtt-----------tctaccctatgt------gcagGTAATTGACAGATCATTTGGTTTCGACACTGCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAG

upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
gtaagttttttttttccttctacattgtggctttaaactcataatttaaacc--ccattagcatcattaattggtaaatttcttc-------tgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
||||  | ||| |   | | |   |  |   ||       | |||  ||     |  ||  ||| || |  ||     | | | |         ||||  |     |   |||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || |||||||| || ||||| ||||||| |||||  || ||||| ||||
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgctta-atagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
||| | | |  |  |||| |      ||   |  |||   |  |  |||      |   |||   | |||| ||  ||  | |||        ||||||   |||| ||||| ||||| ||||| |||||||||||||| |||||||| ||  | || || ||||| || ||||| || ||||||||||  || || ||||| |
gtacgatctgctcctcctgc------gtatttgaaaaaaaaatagctaattattgtc--cattcctgattg-tagcttcatcctgaa-----ctgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG

upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G443985_T03 (Zea mays), 3'ss of exon 8
gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccatt-agcatcatta----attggtaaatttcttctgc----------tgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
||||  | ||| |   | | |   |      |||      | |    | |  |||||   ||| || |    |      ||   | | |||           ||  |     |   |||| ||||| ||||| ||||| || ||||| || || |||||||||||||| || |||||||| || ||||| || |||| |||||  || ||||| ||||
gtaatatgtttctccacattttagtgacatttttgtgtaaaaatggaagatgccatttgacatgatcacatgaacaacgaaccccatatgcgtgaattcaccgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------gtaagttttttttttccttctacattgtggctttaaactca----taatttaaaccccatt--------agca--tcattaattggtaaatttcttctgctgtctcttgctta-atagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
                                        ||  | | ||        | ||     | | | |||| |||     |||||    || |||        | ||  ||  |  || ||  |||| | |  | | || |||||   | |||||||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||| |||||||| | || ||| | || |
gtacatctctttgtttccttaattgctgattataggaccggttggatattacacctgatttattgcatagatataaattcaaaaacaatttttttcctattttttattgaccaattctctttttagttgatttttacctccgactattgctggtacagGTTATTGACAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCCCAACGTGCTATTAATGCAGCACATGTTGAATCTGAAAGTATCGAGAATTGTATTG

upper sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgc--ttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
                          || |     |||||  | | |    ||    |||  ||   |    | ||  | ||| |  |   |  |   |   | |||| ||   | | || |  | || || | ||||||||||| ||||| |||||||||||||| || || || |||||||| || |||||||| ||||| ||||| ||||||    | |||||  | |
gtactatacatcatccctactacacagtgacgcgctttttcacatgtg---tgcttatttccacatgttgcctgaattc-attcgtgtgcgttctgacttgttctcttttgggatttgtttcaatgaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG

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|7691740|gb|AW759862.1|AW759862
EST:     TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCA                         GTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
genomic: TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCAgtaagttttt ... tgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
EST: gi|192321852|gb|FK013230.1|FK013230
EST:     TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCA                         GTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
genomic: TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCAgtaagttttt ... tgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
EST: gi|10237267|gb|BE806155.1|BE806155
EST:     TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCA                         GTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
genomic: TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCAgtaagttttt ... tgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
EST: gi|6566092|gb|AW233852.1|AW233852
EST:     TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCA                         GTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA
genomic: TCAAAGTTTCAGTTGTAGGTATCCCCAAAACCATAGATAATGATATTCCAgtaagttttt ... tgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccccattagcatcattaattggtaaatttcttctgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
              cattaat  putative branch site (score: 3)
                            tttcttctgctgtctc  putative PPT
               attaattggtaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttttttttccttctacattgtggctttaaactcataatttaaaccccattagcatcattaattggtaaatttcttctgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA