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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

Basic information

species Glycine max
transcript GLYMA19G30450.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 3'ss of exon 10
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
|| | | | ||| | ||| || || | | || | | | || |||| | || ||||| ||| | || |||||||| ||||||||||| |||||||||| || | |||||||||||||| |||||| ||||| || |||| || |||||||| | ||
--gttagtattcatggtttagtactttactttgtttag-gattctagcatctgttctctctttgacaattaa-------tgtgtaaatctaaaa-accagCTGGAACCCAGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os12g03530.1 (Oryza sativa), 3'ss of exon 13
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatg--gtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
||| | || | | | || | || || || ||||| || | | | | | | | | | | || |||||||| ||||||||||| ||||| |||| |||| ||||| |||||||| ||||||||||| || |||| || |||||||| | ||
---------gttagtacctcca--gctttgctcctttttatttccaacgttcttgttggtcacaagtacgcgagtttgactagaccttaatgtaatgatcagCTGGAACCCAGATGCAATTGTGTTCAATTCCTGGCAGCAGTATGGCACTCCTAGTTATTGGGTGCAGACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
||| | | || | || | | | | | | | | | | | | | | | | | | | || |||||||| ||||||||||||||||| |||| || | ||||| |||||||| |||||| ||||| || |||| || |||||||| | ||
---------gttagtacctttggctttgccttttttattttctaacattcttcttgttcacaagtgcttgagtttgactagctctgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
|| | | | | | | || | || | | || | | | | | ||| | |||| ||| | ||| | | || |||||||| ||||| ||||| |||||||||| || | |||||||||||||| |||||| |||| || |||| || ||||| || || | ||
--gttagtatacatggtcttatactttctt-tgttcaaggattctagcatctgtttcctctctgactattg-ctaa---tgtataaatgtg-ataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 15
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttc--tgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
||| ||| | || | | || | | | ||| |||| | | | | | |||| || | | | |||||||||||||| || || || |||||||||| |||| |||||||||||||||||| ||| |||| ||||| |||||||| || || | |
---------gttagtattcttggtttttttttaccctctacttgttcttttcccgttgctct-aacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATCGTCTTCAACTCCTGGCAGCACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGTGCCATGATC

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttc--tgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
|| | || || | || | || | | | || | | | |||| || | | | | | | |||| || | | | |||||||||||||| || ||||| |||||||||| || | |||||||||||||||||| ||| |||| ||||| |||||||| || || | ||
--gtta-gtattcttggtt----ttttttaccctctacttgttcttttcccgttgctc----taacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 15
aagtaaagtgttt-tcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
|| | | ||| || | | | ||| || || | || | || | ||| | ||| | | ||||||| ||| |||||||| || || ||||| | ||| || ||||||||||||||||||||||| |||| || ||| | |||||||| |||||||| |||
-------gtatctctcactttagtttcaacggtttttatcggtatatct-tgaatgcggtaatcagaaacaagcccg--ttgcttttgttttgtttttcagGTGGATCCCTGATGCAATAGTTTTTAACTCGTCTCATCTATATGGAACTCCTAGCTATTGGGTCCAACACTTCTTCACCGAGTCAAGCGGAGCAACTCTT

upper sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 15
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
|| | | | | | | | |||| | ||| | | | | ||| || | ||||| | |||| | | ||||||||||| |||||||| || |||||||||| ||| || |||||||| |||||||||||||| |||| ||||| |||||||||| |||||||| |||
-------gtatctctcacttacttttccgttcgaatggttactcaggaaga---------taaggcaataatctcaaattgt-taaatt---ggtttcagGTGGAACCCTGATGCAATAGTCTTCAACTCCTCTCATCTATATGGAACACCTAGCTATTGGGTTCAACGGTTTTTTGCAGAGTCAAGCGGAGCAACTCTT

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|254323777|gb|GR836116.1|GR836116
EST:     ATCCAAATGGCCAGCTATGCTCCAC-TTTTGTTAATGCCAATGATAGGAG                         GTGGAAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGG-AACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTC
EST: gi|23733336|gb|BU764862.1|BU764862
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|23725399|gb|BU760653.1|BU760653
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|10253908|gb|BE821723.1|BE821723
EST:     AGCTATGCTCCACTTTTTGTTAATGCCANNNNTAGGAG                         GTGGAACNNNGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: AGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|33390367|gb|CA853562.1|CA853562
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|15285857|gb|BI469748.1|BI469748
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|13312086|gb|BG405737.1|BG405737
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|22523685|gb|BU082496.1|BU082496
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|21888837|gb|BQ742050.1|BQ742050
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|13181153|gb|BG352493.1|BG352493
EST:     ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAG                         GTGGAACCCCGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|208156031|gb|GD954535.1|GD954535
EST:     AATGCCAATGATAGGAG                         GTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: AATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
EST: gi|15285949|gb|BI469840.1|BI469840
EST:     ATGCCAATGATAGGAG                         GTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC
genomic: ATGCCAATGATAGGAGgtaatttctt ... ctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT
              tcttgat  putative branch site (score: 4)
 tttctgtc  putative PPT
 taaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - - - - - - -catgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgtg