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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatggacttttcttctacactaattctttgataaattttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag...

Basic information

species Glycine max
transcript GLYMA05G32190.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatggacttttc-----ttctacactaattctttgataaattttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag
 ||| | || || || || ||||| ||||| |||||||||||||||||||||||||||||| || ||||||||| ||| |  || || || ||||| || || |||   | |   ||||| |      ||  | ||| | |       |  |||| |     ||       |     |   || | || | ||  |   |     
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaatttcagtacaat-----

upper sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G147450_T03 (Zea mays), 5'ss of exon 10
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatgg-acttttcttctacactaattctttgataaat-tttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag
|||  | || || || || ||||| |||||||||||||||||||| || ||||| |||||  || | || || | ||| |  || || || ||||| ||||| |||   ||  |   |||||| || | |  ||  |   | ||   | ||   |             | |  |   | |   | ||  |  ||    ||  
GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcctacctcttacttttgttatgctttatgtgagtcatgtctgttaaaaacaacttaggaggaactaagtgtcttcgatattaagaaagaaatt--

upper sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G27740.1 (Arabidopsis thaliana), 5'ss of exon 8
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtat--gtgattaa----atggacttttcttctacactaattctttgataaattttgtagtgttccttctccac-catatcttgtgtaa--aatccatgaatcttttag----------------------------------------------------------------------------
 ||||| || || |||||||| |||||||| |||||||||||||||||||| || || |||||||||    ||||||| ||||| || || ||||||||||||    |    ||    |     ||   ||  |  | ||   |   |  || |  | | |    ||||  ||  || |  | |  |||  |    || || |   |                                                                              
AGCTTTGGGGGGTAAAACCTTCAAGATGAAGTTTGGTCATCATGGAGGAAACCACCCAGTTCGTAACAACAGAACTGGTCAGGTGGAGATCAGTGCTCAGgtaccaatacccaacctcaaaatgttccatttaattccaagcatactaccaactaaggatttgaacttccacattcaaagttcggataattatctgataaaacgactgtgctaggaacattgttacaagcttgacaaaatctaaatatggtgtatcattgtctttttttctgtaattcttggcag

upper sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 5'ss of exon 8
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatggacttttcttctac-actaattctttgataaattttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag-
||| || || || ||||||||||| ||||| |||||||| ||||| ||||||||||| |||||||||||||| | ||| |  ||||| || ||||||||||| |||  | |  | ||| | | ||   | | ||||  ||  |  ||  |   | |  ||    |  ||  | |   ||      |  ||  ||  ||  | 
GGCATTGGGTGGTAAAACCTTTAAAATGAAGTTTGGTCACCATGGTGGAAATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgt--tcacctagacctctgtttagctattaatgtttgcaagaacatctaattcctctaattttactttcttcagttccctgtaaattgattcttctgt

upper sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S42_59V6.2 (Physcomitrella patens), 5'ss of exon 9
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgta-----tgtgatt-aaatggacttttcttctacactaattctttgataaattttgtagt-gttccttctccaccatatcttgtgtaaaatc-catgaatcttttag
|||  | ||||| |  || || |||||||||||||||||||| || ||||||||||| |||||  || | |  || ||||  || ||||| ||||| |||||        ||||| || |  |  |||   || |   || |   || | |  |||||  | | |       ||  |  |  |||| | |||  || | ||       
GGCACTTGGAGGTACGACATTCAAGATGAAATTTGGTCATCACGGTGGAAATCATCCAGTTCGCCACTTGCCCACCGGCCGCGTGGAAATCAGTGCCCAGgtcatagtcatgattcaagttcatcttttgacttctgcaaatacatgctga-ctttgtgctagattacatgacataaagttctgtgcagaatgacacggat-------

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|20812899|gb|BQ297377.1|BQ297377
EST:     ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAG                         AACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgatt ... tcattggcagAACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
EST: gi|254323386|gb|GR835887.1|GR835887
EST:     ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAG                         AACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgatt ... tcattggcagAACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
EST: gi|254343190|gb|GR859352.1|GR859352
EST:     ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAG                         AACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgatt ... tcattggcagAACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
EST: gi|31456627|gb|CD398655.1|CD398655
EST:     ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAG                         AACCACTACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT
genomic: ATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgatt ... tcattggcagAACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatggacttttcttctacactaattctttgataaattttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccacc