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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG

Basic information

species Glycine max
transcript GLYMA10G38150.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g35870.1 (Oryza sativa), 3'ss of exon 1
--tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttat-cacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
  | |||   ||   ||  | |  | ||||   | |  ||| || |||  ||  |  ||||  || |||| |||   || ||| |      |      | ||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||||||  | || |||||||| || ||     | ||| |||| || 
attgttgcattgcccctaatattctgttttgaaagtggatacttaaat--atttt-ttaactgtgtttctaattaccattcacattttgacggccatatgcagGATGTTCTATGGACCTGGTGGACCTTATGCGCTATTCGCTGGCAAAGATGCCAGCAGAGCACTCGCTAAGATGTCCTTCGAGCCCCAGGATTTGACCGGT

upper sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g42740.1 (Oryza sativa), 3'ss of exon 1
--------------------------------tattgtgctgatgcttttttctttt----tttttcattacatattttaattg-atagtgctaac----actgc------ttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
                                 |||     ||  |||| || | ||      |  || ||| |||    |||| | |   ||| |     ||||      ||| |   | | |||  |   ||        | ||||||||| |||||||||||||| || || || || ||||| ||||  |||||||| ||||| || ||||||||||| || ||   | | ||| | || || 
gtaggcttccttcatttcttgggtaccgtaaaaattcgatcgaaactttcttttcttggatcatggcactacctatgaccattgcaaatcactagctctagctgcaaaatgttcgtccatatttcatctttcatctccgttttgcagGATGTTCTATGGACCTGGTGGCCCATACGCACTGTTTGCAGGCAGAGATGCTAGTAGAGCTTTGGCGAAGATGTCCTTCGAGCTGGATGATTTAACCGGC

upper sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G107444_T01 (Zea mays), 3'ss of exon 1
tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttatcacgtgga---attgtgtccc-tccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
  |||||   ||   | | |||   |         |    ||   ||  |  | |  |   ||  |  | | ||||| | ||  |   ||||   ||  | ||| ||||| ||||||||||||||||| || |||||||| || ||||| || || ||||||||| ||||||||||||| || ||     | |||||||| || 
agttgtg--aatcaatctctctcagtccacagccccgcccttcttttacttttac--atgttgaattctgtatttataatgtttatcaattgacccctgtgcagAATGTTCTATGGACCTGGTGGACCATACGCCCTATTCGCCGGCAAAGACGCCAGCAGAGCCCTAGCGAAGATGTCCTTCGAGCCACAGGATCTGACCGGC

upper sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G882228_T02 (Zea mays), 3'ss of exon 1
------tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
        |||||| |||    ||  |         |    | | | ||| ||   |   | |   ||| | | | |     |   ||  || ||   |    ||| ||||| ||||||||||| |||||||| ||||| || || ||||| ||||| ||||||||  ||||||||||||| || ||     | || || || || 
aaggacagttgtgcagat----ttggcgagcacccccggcccttttcttactttgcatatcgagttctg-tacatgtaacagtt-tgttaaaatgaccctacgcagAATGTTCTATGGACCTGGCGGACCTTACGCCCTGTTCGCCGGCAAAGATGCCAGCAGAGCTCTAGCGAAGATGTCGTTCGAGCCACAGGACCTCACCGGC

upper sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S97_92V6.1 (Physcomitrella patens), 3'ss of exon 2
-------tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
       ||  | |  |       || |   |  | |  | |    | | || |  |  || | ||     ||  | |  ||   ||  | |  | |||     ||||   ||||| ||| |||| |||||||||||||| || ||||| || || || || ||||| || || || ||||||||||| ||||| |||||||| || 
tatttcttacggaggagcgatgacttgccactagtgtggtcagggttctaaactatt--tgttgac-----tttctgtagttcaaaccggaatgtctgttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT

upper sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S38_353V6.1 (Physcomitrella patens), 3'ss of exon 6
--tattgtgctgatgcttttttctttttttttcattacatat--tttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
   || ||     | |     ||| |  |||     || |||  | |||  ||||   ||       |||  |||      | | |||||     ||    ||||   |||||||||||||| ||||| || || || |||||||| || || || ||||| ||  | || || ||||||||||| ||||| ||||||||||| 
agaatcgtctctcttccgaggtctatcgtttgagagacctatcatgtaacggataa-acttctgagacttactatggaacgctcctggaac---atcgtaacagGGCATTTTATGGACCTGGCGGACCATACGCACTCTTTGCTGGGAAAGACGCCAGCAGGGCTCTGGCCAAAATGTCTTTTGAGGAGAAGGATCTGACTGGC

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|254331808|gb|GR846118.1|GR846118
EST:     CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAG                         GATGTTTTATGGAACTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
genomic: CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAGgtttactgtc ... gtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
EST: gi|6667370|gb|AW278821.1|AW278821
EST:     CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAG                         GATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
genomic: CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAGgtttactgtc ... gtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
EST: gi|18041207|gb|BM309501.1|BM309501
EST:     CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAG                         GATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
genomic: CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAGgtttactgtc ... gtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
EST: gi|18692769|gb|BM521617.1|BM521617
EST:     CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAG                         GATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
genomic: CCCTTGCTCATGGCCATCAAGGCCCAGATCTATGATGTCTCCCAGAGCAGgtttactgtc ... gtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
EST: gi|207706620|gb|GD688568.1|GD688568
EST:     ATCTATGATGTCTCCCAGAGCAG                         GATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC
genomic: ATCTATGATGTCTCCCAGAGCAGgtttactgtc ... gtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
       tgctaac  putative branch site (score: 1)
                                            tgtccctcc  putative PPT
                   ttcttatttttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - -ctgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacgtgg