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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

Basic information

species Glycine max
transcript GLYMA01G43910.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 2
----gttgaatgtctatatggtattggcgccgcttgttag---ttttggccagcaaatgagtctacataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
    ||| | | || ||       |  | |||| |  | |    |||          |||| | |    |       |      |    ||    ||   | |||||| ||||| |||||||||||||| || ||||||||  | ||||| || ||||||||||| || || || ||| | |||||  | ||||||||||||||  |
gtaggttcactctc-atccctccctccctccgcctcatcgaatcttttattttgttttgagccaaatccaaacccaacctaacatcatcatcatcatcatcatgcagGCTTCAACGTGGAGAAAGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
---------------------------------------------gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctaca--taatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
                                              || ||    |      ||  |  | |      |     || |  |||| ||| ||  |   | || | | |   |           | |||  | ||| |||||||||||| ||||| ||||| || ||||||||  | ||||| || ||||||||||| || || ||||| || ||||| || ||||||||||||||  |
gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactctgcacctgccatgcaattgattcgtccgttcatatgtttagtgacagcatgcactttatcacattgtagGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacata-atgtttctctaggtttttaaatttatattgc--cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
     ||||   ||  |  ||   |  | ||  ||    |    |     | | | | | |  |  ||  | |  | |  ||  | | |  |||  ||   |||||||||||| ||||||||||| || |||||||| || || || || ||||||||||| || ||||| ||  | |||||  | ||||||||||||||  |
ccaatatgttcttaaaggttttatgaggattactaaaaata---aatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 2
gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacata-atgtttctctaggtttttaaatttatattgcctt--gcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
  |   |||||  || | |  |||   |||  |    ||        ||   | | | | |  |  ||  |||  |    ||  | | |  |||  |    ||||||||| || ||||||||||| || |||||||| || || || || ||||||||||| || ||||| ||  | |||||  | ||||||||||||||  |
--ttcctgtcttaattgaaa-ggcagggctcctgccattacatttaaaacaaactttccctgcaaattcgtctgtgacgatatgtctctggtgctatcactagGTTTCAACGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtct-acataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
   | | ||| | || |     ||     |  ||  |||  |    |  ||   ||| |||    ||||    ||| |||||||||| |         ||||||||||||| |||||||||||||| |||||||| || |||||||| ||||||||||| || |||||||| || |||||  | |||||||| |||||  |
---gtaggtc-agattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttct-----tacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgaatgtctatatggtattggcgccgcttgttagttt--tggccagcaaatgagtctacataatgtttct-ctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
 |    || |  |||  | ||  |   | || ||  | |         |   ||  | |    | | | ||| ||     |||||| |||| || |    |||| |||||||| |||||||||||||| |||||||| || |||||||| ||||||||||| || ||||||||||| || || ||||||||||| |||||  |
ttcttgtgacattatacttttatctatgattattgttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttact---cagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
-gttgaatgtctatatggtattggcgccgc-ttgttagttttggccag-caaatgagtctacataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
       ||   |||| |||   |        | |   | |||    | | ||||   || || | || || |     ||  | | ||| |  |    |  ||||||||||||||||||||||||||||||||| || || |||||||| |||||||| || |||||||||||||| |||||||| |||||||| |||||| |
taacagttgatcatattgtacatgtattatactatggatgttgatgtgtcgaatggagcttcagattgatttt---aattgatcattttctggtaatatatagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacataatgtttctctaggtttttaaatt-tatattgc------cttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
                                                                              ||    | ||||   | |||   |||  | ||   |       |||  ||||| |   | | | |    |  |||  ||||||  || || |       || |||| |||||||| ||||||||||| || |||||||||   || ||||| ||||| |||||||| ||||||||| |  | || || ||| |||| |||||  |
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccg--tatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------gttgaatgtctatatggtat----tggcg-----ccgcttgttagttttggcc--agca--aatgagtctacataatgtttctctaggtttttaaatt-tatattgcc-----ttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
                                                                   |||||| ||   | || |||    ||  |       ||   ||| | |||  |  |||    |||||||  |    | | |    |  | || |  |  | | || ||     |  |||| || |||||||| |||||||| || ||||||||    |||||||| |||||||||||||| || |||||| |  |||| |||||| |||| |||||  |
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------gttgaatgtctatatggtattggcgccgcttgttagttttg---gccagcaaatgagtctac-ataatgt--ttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
                                                                                 ||   || |  | |  | || |      |  |  || | |   ||  |  |||  |  | | |  ||||  ||   || ||| ||    ||||      || |||| ||||||||||||||||||||||| ||||| ||    || ||||| |||||||||||||| ||||||||| |  |||| || ||| |||| || ||  |
gtagcttgacttaacacttccagttgatccttttgtatttgaaagagcccctcttcgtttctgcttatttgatgtatttgcttatttgacggtgttttgtttgatgtattattctgtgtcgagtgctggtgaatttgctttcgaggatgtcatttgttaagttgttgtggttatgcaatatt-cagGGTTCAATGTGGAGAAAGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAA

upper sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
gttgaatgtctatatggtattggcgccgcttgttagttt--tggccagcaaatgagtctacataatgtttctctaggtttttaaatttatattgccttgc-agGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
                    |    |   ||  | ||||  ||||   ||  |    || | |  |   | ||| |  |     || |  ||  |||||| ||| || || |||||||| || ||||| ||||||||  | ||||| || ||||||||||| || || ||||| ||||| || || |||| ||||||||||  
-------------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgact----gatgtgaat--ccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

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|151396333|gb|EV266210.1|EV266210
EST:     ACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGG
genomic: ACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGG
EST: gi|254345773|gb|GR859420.1|GR859420
EST:     ACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGG
genomic: ACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGG
EST: gi|151393667|gb|EV263542.1|EV263542
EST:     ACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG                         GTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGG
genomic: ACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTGgtgggtctta ... tgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatgagtctacataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA
                                            ttgcctt  CT-rich tract
                        tctaggtttttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtctacataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG