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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag...

Basic information

species Glycine max
transcript GLYMA05G25320.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaata-ttat-atggacgtagtggtagaaattagaaaaatag
| |||||||| || || ||||||||||||||||| || |||  ||||||||| |||||||| || ||| | || || ||||| ||| | ||||| || ||||      |||     ||   | || || ||||   | |  |  |  ||   || |  | || || | || | ||||  | || |  |  | |   |  |  
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaaccaaccctctgctgctcttgtttaggactttggattcacttattaggagtagtcatcacggactgattgattcat-tgattgatgtg-

upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 1
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgta---tataatatatctgaagaatgtgttggtcttcaattgtg-caattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag---------------------------
| |||||||| ||||| ||||||||||| ||||| || |||  ||||||||| |||||||| || ||  | || || ||||||||  | ||||| || ||||     |     |  ||      |   |   |||     || | |  ||  |  | || |   |   |||  |||||    ||| |      |     |||                             
TCAAGAAGATCCGCCTGGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCGCTGCTCAAGGAGATGCAGCATCGCAACATCGTCAGgtgacccacctcctccctccctgctagctccatctctctctgcggctgttggttgggtgggtgggtggattg-atggattgcgtgatttgcgatttgtgaatgctttgggaatttggattgtgccgtgcag

upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G174596_T02 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctga-agaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag
| |||||||| ||||||||||||||||| ||||| || |||  ||||||||| |||||||| || ||| | || || ||||||||| | ||||| || |||||  ||   |  | |  ||  |||||| |   |  |     |      | |||||   |   |     |   |  |  |||  ||               
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCCCTCCTCAAGGAGATGCAGCACCGCAACATCGTCAGgtacgtacgttgccagtcaggttgtgttcggagtgcaggcccccccggctatgctgctcactcacgcgctcccg-tgccgtg-cag---------------

upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaa----tgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag
| |||||||| ||||||||||||||||| ||||| || ||   ||||||||| |||||||| |||||| | || || ||| | ||| | ||||| || ||||          |     |      |   ||    | |   | |   |||  |||  | |  | | || |    | ||   |  ||  ||              
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg----

upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctg---aagaatgtgttggtc---ttcaattgtgcaattcatgtgctgagaaagaatatta-----tatggacgtagt--ggtagaaattagaaa-aatag-------------------------------------------------------------
| |||||||| ||||||||||||||||| ||||| || ||   ||||||||| |||||||| |||||| | || || ||| | ||| | ||||| || ||||      |   | |    || |  | || |||    ||  |   ||  |||| | ||||       |||  |      |||| | | | |   ||| || | |||   |||                                                               
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgctcgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag

upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatg-tgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag
||||||||||  | || |||||||||||||| || ||||| ||||| || ||  | || || || ||||||||||||||||||||||| |||||||| | ||||     || |    |  || |||||       |||  |||  | |||   |||  ||| ||| ||  || || ||  |  |   |   ||        
TGAAGAAGATCAGGCTAGAGCAGGAGGATGAAGGTGTTCCTAGCACAGCAATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatg----atgttaataccat-tgttgaaaactgattcagca--tgatgactctggtaaacaattttg-attgatgttttt-tgctacacag--------

upper sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag
|||| || || || || ||||| || ||||| || ||||| |||||||||||||| || ||||| ||| ||||||||||||| ||  | ||||| ||| |||| |   |      ||      | | |   ||    | |||   |  | ||       ||| | | ||       |   ||       ||     |   
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctcagcacgactggattttagaatttgcgatatgctcctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc

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|193414159|gb|FK377859.1|FK377859
EST:     TCGCGAGATTTCTCTCTTGAAAAGAAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: TCGCGAGATTTCTCTCTTG-AAAG-AAATGCAGCACAGGAACATTGTTAGgtatataata ... tggaacgcagGTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|16996519|gb|BM085891.1|BM085891
EST:     ATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATGCAGCACAGGAACATTGTTAGgtatataata ... tggaacgcagGTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
EST: gi|254326865|gb|GR836474.1|GR836474
EST:     ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataata ... tggaacgcagGTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA