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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG

Basic information

species Glycine max
transcript GLYMA15G15310.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------------cttcttgaccgtatttaactcttaccttt--ttctctagttgcattgctgttctttacttgctttattgttt---------actaactacttttaagctgt---tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | | | ||| | ||| | | | || |||| | | || | | | ||| || | | | | | | || | ||| | ||| |||| ||| |||||||||||||||| || || |||||||| ||||| || |||||||||||||| ||||||||||||||||| || || || || | |
gtgattctacttttccaccttattgtattctagacctaaactgtttcttataatcacattggatccttgcaatgaatactgtagtcagactaatgctaaagaggaaatctatccttggaacttgaaaatgatgagacatgaactctacttttgctacagATGATTTACCGGCCTGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCG

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 12
----------------------------------------------------------------------------cttcttgaccgtat-ttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
||||| | | || | | | | || || | |||||| ||| || || || || | | || | || || | | |||| |||||||||| ||| |||||||||||||||| || || || || || || || || ||||| |||||||| ||||||||||||||||| ||||| || || |||
gtatacatgtttttagtttgtgccacttatttctatcagttttttttccttgcagggttatttctatcagttgtgttgtcttgtctccaaattggcacctgggtattgctgtc-ttgcatggct--tcattcagtgacatactttgggcttgacaattgtatgttcctttc-tgcagTTGATTTACCGGCCTGACACTGGAGAAATTCTTGGTGTGCACATTTTGGGTTTGCACGCTGCTGACCTCATCCACGAGGCATCAAATGCCATTGCCCTAG

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 12
--------------------------------------------------------cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
||| | || | | | |||| | |||| || | | | | | | | | | | || | | || |||| ||| |||| || | |||||||| ||||| || || ||||||||||| || || ||||||||||||||||||||||| |||||||| ||||| || || | |
gtagtaatgcggtagtgtgtttccaccctgttgcattctaaatttatgcacggagaattccagtggatacattaaccagacctatg---ctagggagcctg-tatccatggaacctctaaatttgaagtgacgatacatgtactattttgcctcagATGATTTATCGCCCTGACACCGGAGAAATTCTTGGAGTTCATATTTTGGGCTTGCATGCTGCTGATCTCATCCATGAGGCATCAAATGCCATTGCCCTTG

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 12
--cttcttgaccg-tatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaa--ctacttttaagctgttttca-tgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | || | || || || | | |||| | | | |||||||| ||| | || || | | || | || ||| |||||||||| ||| | |||||||| || || || || || ||||| || || || |||||||||||||||||||| ||||||||||| ||||| || || |||
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttt-tcattaacagaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 12
--cttcttgaccg-tatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaa--ctacttttaagctgttttca-tgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | || | || || || | | |||| | | | |||||||| ||| | || || | | || | || ||| |||||||||| ||| | |||||||| || || || || || ||||| || || || |||||||||||||||||||| ||||||||||| |
gtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttt-tcattaacagaatttgacaatatgtggtcctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAA---------------

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 12
cttcttgaccgtatttaactcttacctttttctc---tagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatg----cagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| || | || || | |||||| || ||||| | | ||| | | | || | | || | |||||| ||| |||||||||| ||||||| ||| || || || ||||||||||||||||| ||||||||||||||||| ||||| || ||||| || || || || ||||
-gtgaagagaagaaccaaaaattgaaataaaaaaagatagttgtat-atagttctggagtgacttg--cgaagataagatatctgaacactctcttcatgtgaacagATGATATACAGACCTGACAATGGTGAAATCCTTGGAGTTCATATATTTGGATTGCATGCTGCTGATCTTATCCATGAAGCATCAAACGCGATTGCTTTAG

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 12
cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | | | || | || | || | || || | ||||| | || || | | || || || || || |||||||||| ||| |||| || || || |||||||||||||||||||| ||||| || || || || |
------------------------------------------------gtaataaaataattcgtcgtaacacggttgatt--gatttgattcc-tgcagCTTATTTATCGCCAAGATACCGGGGAAATCTTGGGAGTTCACATAATTGGCTTACACGCAGCTGATCTCATCCACGAGGCTTCCAACGCCATGGCTTTGG

upper sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 12
cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
| | | | || | || | || | || || | ||||| | || || | | || || || || || |||||||||| ||| |||| || || || |||||||||||||||||||| ||||| || || || || |
------------------------------------------------gtaataaaataattcgtcgtaacacggttgatt--gaattgattcc-tgcagCTTATTTATCGCCAAGATACCGGGGAAATCTTGGGAGTTCACATAATTGGCTTACACGCAGCTGATCTCATCCACGAGGCTTCCAACGCCATGGCTTTGG

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|5509415|gb|AI855973.1|AI855973
EST:     NAGCT-ACACAAAGGCCTTAGCTGAAACCGAAGCGTAGGGTCTTGCCAAG                         TTGATATACAGGCCTGACACTGCAGAGATACTGGGAGTTCATATATTTGGG
genomic: AAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAGgttatatttc ... tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGG
EST: gi|19054208|gb|BM732875.1|BM732875
EST:     AAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAG                         TTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGG
genomic: AAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGGAGGGTCTTGCCAAGgttatatttc ... tttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG
                        tactaac  putative branch site (score: 0)
 ctgttttc  putative PPT
 tttattgtttactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttgaccgtatttaactcttacctttttctctagttgcattgctgttctttacttgctttattgtttactaactacttttaagctgttttcatgcagTTGATATACAGGCCTGACACTGGAGAGATACTGGGAGTTCATATATTTGGGTTGCATGCTGCTGATCTCATCCACGAGGCATCCAATGCAATAGCATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
cttcttg
- - - - - - - - - - - - - - - - - - - - -attgctg