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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaaactt...

Basic information

species Glycine max
transcript GLYMA13G35580.1
intron # 3
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatcctt-----ttcttat----cgatatcttaattagctt-aattcaggcatgaagaaa-tgatttgggagtgtgaa-taatgagaattgatttgactgtagttaaactt---------------------------------------------------------------
  || || || || ||| | || |||||  |||||||||| || ||||||||||| || || || || |||||||||||| | || || |||||||||||     || ||||     ||  ||||  |  | || || ||  || |     || |   |||||| |   |    |||   ||    ||| || | | | | | |                                                               
CTGGTAAGACAGACTACAGGGCAAGGATAAGGTTGATTAACCAAGACAAGAACAAGTACAATACACCCAAATACCGATTTATTGTGCGATTTgtatccttcaaatttattatttggtgacttcttgttgggtttcaactctagcctaccccaacttgcttgggactaaaaggctatgttgatgttgttgtcttttgatcatcctcctgcttattattttggcactttaagcattggcggcattgtatctcttaataaatctccttag

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaattcaggcatgaagaaatga--tttgggagtgtgaataatgagaattgatttgactgtagttaaactt
  || || || || ||| | ||||||||  || ||||||| || ||||| ||||| || ||||| || |||||| ||||||| || || ||||||||||||  ||||       |    |  ||   |   |  |||      |||  |   | ||  |  ||  |     || | | || | |  |||     
CTGGCAAGACAGACTACAGGGCCAGGATAAGGCTGATTAACCAAGACAAAAACAAGTACAACACACCCAAATACAGATTTGTTGTGCGATTTgtatcctttgattatttgaccatctggtttctacctattgctatggtactttgagctccagaagcatatattgtatctcttaactaga-tattcttag----

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 4
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaa--actt---
 ||| || || || || ||||||||||||||  |||| ||||| |||||||| || || |||||||| ||||| |||||||| || || ||||||||||  | | |    |   |  | |   || || |  |  | |     ||        || ||  |||| |  || |     || | | || |  ||||   
CGGGCAAGACAGACTATCGTGCCAGGATTCGCCTGATCAATCAAGACAAGAATAAGTACAACACTCCAAAATATCGATTTGTCGTGCGATTTgtatcctaatatcaagtttgattctact--ttttatgcgtgtgt-actggttggccctctggtatg--taattaagatgggagacacagaaatttattacttaaa

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaaactt-------
||||||| || || ||| | || ||||||||  |||||||||| ||||||||||| ||||||||||||||||| || ||||| || || |||||||||||   ||||    ||  || ||  | ||||||     |   ||  |    | |  || | |||||      |||    | ||   || || ||        
AGGGAAAGACTGACTACAGGGCTAGGATTCGCCTGATTAATCAAGACAAGAACAAGTATAACACTCCGAAATATCGCTTTGTTGTGCGATTTgtatccttaatttattataataatatttc-cataattc-----ttctgatttccccttgtggt-tcaataagctaggttgtcgaggcttctgtcaacctcttttgtt

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttg--ggagtgtgaataatgagaattgatttgactgtagtta-aactt--
  || |||||||||||||| || ||||| || ||||  | ||||||||||||||| || ||||| ||||| ||||| || || ||||| || |||||||| |    || | || |||   ||   ||  |        |||| | |   |  | ||| | | |  |   | ||   |||   |  || | |||||  
CTGGTAAAACCGATTACCGGGCGAGGATCCGTTTGACCACTCAGGACAAGAACAAGTACAACACCCCGAAGTACCGTTTCGTCGTTCGTTTCgtatccttctgac-tctacattttag--agtgcaacgctactggacagaagttaaaagatgtagtttcactcttttaattt--cttgttgggggtgacaacttca

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S97_115V6.1 (Physcomitrella patens), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttct-tatcgatatcttaattagcttaattcaggca-tgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaaactt
  ||||| ||||| ||||| || ||||||||  |||  |  ||||||||||||||||| ||||| ||||| ||||| || || || || ||||||||||||| | | | | | |  | || ||  |  ||  |  | |      |  ||||| |||    |  |  | |  ||  ||  |  |||  |   |  
CTGGAAAGACCGACTACCGAGCTAGGATTCGCCTGACCACCCAGGACAAGAACAAATACAACACCCCGAAGTACCGTTTGGTCGTGCGATTTgtatccttttatgtgttgctttgatcatgaggatctttttgcaagtcgttccaacatttgagagaactatgacggtggcttttttgaagcgtatctgttc--

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S38_329V6.2 (Physcomitrella patens), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaat--tcaggcatgaagaaatgatttgggagtgtgaataatgagaatt-gatttgactgtagttaaactt
  || ||||||||||||||||| |||||||| |||| ||  ||||| |||||||| || ||||| ||||| ||||| | ||| || || |||||||||||| | ||     ||  |   | || | ||  || ||  | |   |  | | ||   |  |      |  | ||| |  ||   ||| | | | || 
CCGGTAAAACCGATTACCGTGCGAGGATTCGTTTGACTACCCAGGATAAGAACAAGTACAACACCCCGAAGTACCGTTATGTCGTGCGATTTgtatccttt-catactacaattctggct-gcgtgatggtctgggtttagtgatggctgtgcccgcctcgtcgttttggattagggttcggtgt-gctgaccta

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: EFJ31187 (Selaginella moellendorffii), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttt-tcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaaactt
|||| || |||||||| || ||  || | || ||||  |||||||||||||||||||| ||||| ||||| |||||||| || ||||||||||||   | | |||  |  ||   ||    | ||  |   | || |       |  ||| | | | ||  | |                             
AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTTgtaagttctgtctcctttatcatttggaaaactgga--aaagcttacgttttttgttttg-attttgtgttag----------------------------

upper sequence: GLYMA13G35580.2 (Glycine max), 5'ss of exon 3
lower sequence: EFJ17161 (Selaginella moellendorffii), 5'ss of exon 3
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttt-tcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaaactt
|||| || |||||||| || ||  || | || ||||  |||||||||||||||||||| ||||| ||||| |||||||| || ||||||||||||   | | |||  |  ||   ||    | ||  |   | || |       |  ||| | | | ||  | |                             
AGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTTgtaagttctatctcctttatcctttggaaaactgga--aaagcttacgttttttgttttg-attttgtgttag----------------------------

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|193513631|gb|FK467861.1|FK467861
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCA
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatcctttt ... tggttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCA
EST: gi|6072732|gb|AW102119.1|AW102119
EST:     AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTT                         AGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCCGGCGAT
genomic: AGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatcctttt ... tggttactagAGCAACAAGGACATTGTTGCACAAATAATATCTGCTAGCATTGCCGGCGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTGGTTCGCTTTgtatccttttcttatcgatatcttaattagcttaattcaggcatgaagaaatgatttgggagtgtgaataatgagaattgatttgactgtagttaaactt

- - - - - - - - - - - - - - - - - - - - - - -  AAGAAC