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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

Basic information

species Glycine max
transcript GLYMA14G06340.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gtaggatgaatattggcaaaaatttcattaga-tatcagttgttgcatgccataacactaatgggaaatttcattgatatgc-tatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||  | |   ||| |       ||  ||| |  |||||||| |    ||    || | |  ||     ||| |||  |||   || ||||||||||  | | |||||||||||| || ||| |||||||||| ||||||||||| |||||||| |||||||| ||||||||| | ||||| || ||||
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattt-tgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gtaggatgaatattggcaaaaatttcattaga-tatcagttgttgcatgccataacactaatgggaaatttcattgatatgc-tatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||  | |   ||| |       ||  ||| |  |||||||| |     |    || | |  ||    ||||||||  | |   || ||||||||||  | | |||||||||||| || ||| |||||||||| ||||||||||| |||||||| |||||| | ||||||||| | ||||| || ||||
gtttgtttcttatggcagggccttctattggtctatcagttttgctccgtttcaaaattt-tgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
-----------gtaggatgaatattggcaaaaatttcattagatatcagt--tgttgca-tgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
            | | |    ||||     |     | ||  |||  ||   |||| || | || |  ||  |||  ||  | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||||||||| || |||||||| ||||||||| | |||||||| ||||
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgat-tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
-gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatg-----ggaaatttcattgatatgct---------atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
  ||| ||    || |  |   ||||| ||||    |  |   |  | ||| |    | |||        |||| | | ||   || |         | ||||||||||  | | |||||||||||| |||||| |||||||||| || || ||||| |||||||| |||||||| ||||||||| | ||||| || ||||
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
--------------gtaggatgaata--ttggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct----atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
              | |   | | |   || ||  |  ||  ||   |   | ||| |   || || |  | | ||     | ||   ||| |   ||    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||| |||||||| |||||||| ||||| ||  | ||||| || ||||
gttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
---------gtaggatgaatattggcaaaaatttcatt--agatatcagt--tgttgca-tgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
           | ||   | || | |     || || |    |||  ||   |||| || | || |  ||  |||  ||  | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||| ||||| || |||||||| ||||||||  | |||||||| || |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgat-tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||||    | | |    | ||     |||     ||| ||    ||| ||| ||  || ||      | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||| ||||| || |||||||| ||||||||  | |||||||| || |
gtagtgc-actttgaatagaagccctatt-----tcaattc---catcccaaaaatctgat------tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||||    | | |    | ||     |||     ||| ||    ||| ||| ||  || ||      | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| |||||||||| || |||||||| |||||  | |||||||| ||||||||  | |||||||| || |
gtagtgc-actttgaatagaagccctatt-----tcaattc---catcccaaaaatctgat------tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
-----------gtaggatgaatattggcaaaaatttcattagatatcagt--tgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG-----------------------------------------------------------------------
            | | |    ||||     |     | ||  |||  ||   |||| ||   | |  ||  |||  ||  | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| ||||| |||| || |||||||| |||||  | |||| ||| ||||||||| | ||||||   ||||                                                                       
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgat-tcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtaggatgaatattggcaaaa--atttcattagatatcagttgttgcatgccataacactaatgggaaatttcat-tgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
||  || |   | ||   |     |||  ||  |||  |     ||     ||| ||  |||       |||| | |||| |     ||||||||||| | |||||| | || || || |||||||||||||| ||||||||||| |||||||||||||| ||  ||||||||||||| || || || |
gttagaagctgactgatgactttgtttttttctataaaaacaactgagctacattac-ttaacaattggtttcttctgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
---gtaggatgaatattggc--aaaaatttc-attaga----tatcagttgttgcatgcca---taacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
     ||| |||  ||||    || | ||||  ||| |    |||||   || || |  ||   ||   || |||   | ||    |          ||||||||||| | || ||| | || || |||||| |||||||||| ||||| |||||||||||||| ||||||||  |||||||||||||||  || || |
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

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|298199409|gb|HO042772.1|HO042772
EST:     TCCTTGCACTTCATGTGGACCATGCACGTGTTGTTGACGTCATGCGGAAG                         GCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGC
genomic: TCCTTGCACTTCGTGTGGACCATGCACGTGTTGTTGACATCATGCGGAAGgtaggatgaa ... tatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGC
EST: gi|6481487|gb|AW200758.1|AW200758
EST:     TCCTTGCACTTCGTGTGGACCATGCACGTGTTGTTGACATCATGCGGAAG                         GCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAAC
genomic: TCCTTGCACTTCGTGTGGACCATGCACGTGTTGTTGACATCATGCGGAAGgtaggatgaa ... tatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAAC
EST: gi|208310285|gb|GE105533.1|GE105533
EST:     TCCTTGCACTTCACGTGGACCATGCACGTGTTGTTGACATCATGCGGAAG                         GCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAAC
genomic: TCCTTGCACTTCGTGTGGACCATGCACGTGTTGTTGACATCATGCGGAAGgtaggatgaa ... tatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcagttgttgcatgccataacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
                                 aaatttcattgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatgggaaatttcattgatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG