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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA

Basic information

species Glycine max
transcript GLYMA03G39130.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
gtgagtacagtgacattttgatttatcttctattta-aactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatac----agATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
|| || | | || | | || | | | || | | |||| | || ||||| | | ||| || | | | | || |||||||| ||| ||||||||||||| ||||||| ||||||||| | |||||||||||||||||||| |||| ||| | || |||||||| |||||
atgt-tatgggcatgcttccagc-actttaaactcatgtcttgttctatattttgatttcatgatgcac-tacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
--gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
| ||| |||| ||| | | || | | ||| | ||| | | | | || | | | ||| | ||| ||||| ||| ||| | || ||| |||| || ||||||||| | ||||||||||||||||||||| |||| || || || |||||||| || ||
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------------------gtgagtacagtgacattttgatt--tatcttctatttaaactaggtgg-atatcat-atttaagaaatgca-tgtgcctaatttagaaaattttcca----ata-cagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
|| | | | || | | || | | ||| | | | | | || |||| || || | | | ||| || | || || | | ||| ||||| |||||||| | |||||| ||||||||||||||||| | ||||||||||||||||||||| |||| | | || |||| ||| |||||
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: AC217311.3_FGT007 (Zea mays), 3'ss of exon 1
gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgca-tgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
| || | || | || | |||| | ||| | || | ||||||||||||| ||| | |||||| ||||||| ||||| ||| | |||||||| |||||||||||| |||||||||| || |||||||| |||||
--------------------------------------------gtatgcattcttccatgttcacagcatctttaat---aataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 7
---gtgagtac-agtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
|| | || || | | ||| | ||||| | || | | | ||| ||| | |||| | ||| | || | ||||||||||||| ||| | |||||| ||||||| ||||| ||| | |||||||| |||||||||||| |||||||||| || |||||||| |||||
tgacagactgttagggataacacaacctatga-caatttataataactacgtttgtcctttcttccatgttcacagcatcttta-ataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 7
gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
|| || | | | | | | |||| | ||| | || | ||||||||||||| ||| | |||||| ||||||| ||||| ||| | |||||||| |||||||||||| |||||||||| || |||||||| |||||
------------------------------------------gtatgcattct-tccatgttcacaacatctttaat---aataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 4
-----gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgca-tgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
| | | | | || || | | ||| ||||| || | | || | || | |||| | ||| | || | ||||||||||||| | | | |||||| ||||||| ||||| ||| | |||||||| |||||||||||| |||||||||| || |||||||| |||||
caaaagcatctttaataatatacctatg-acaatttataataactatgtttgtcctttcttccatgttcacagcatctttaat---aataatatacctctgcagATATGGTGTTTCTAGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------------gtgagtacagtgacatt-ttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaa----tttagaa--aattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
| || | ||| | || | | | || | || | | ||| ||| |||| | || |||| | ||| | || | ||||||||||||| ||| | |||||| ||||||| ||||| ||| | ||||||| |||||||||||| |||||||||| || |||||||| |||||
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccattggattttcttatatggcgattgtgatgaaaaaatttcctcaggaatcacagaagtgattctctcgtcgtttgacagatatggatgttcacaacatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGTCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G170845_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------gtgagtacagtgacatt-ttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaa----tttagaa--aattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
|| | ||| | || | || | || | || | | ||| ||| |||| | | |||| | ||| | || | ||||||||||||| ||| | |||||| ||||||| | || ||| | |||||||| |||||||||||| |||||||||| || |||||||| |||||
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccactggattttcttatattacgattgtgatgaaaaaatttcctcatgaatcacagaagtgattctctcgtcgtttgacagatatggatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTATCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S201_115V6.3 (Physcomitrella patens), 3'ss of exon 7
gtgagtacagtgacattttgatttatcttcta-tttaaactaggtggatatcatatt-taagaaatgcatgtgcctaatttagaaaattttccaat---acagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
|| | |||||| | || || ||||| | | | | | | | |||| || || || || | || ||| |||| | || || |||||||||||| |||| ||||| || |||| |||||||| |||||||||||| |||| || |||||| |||| | ||||| |
---cttattggacgtttttgagtagaggtcgggcttcaactatgagcaccctgaagcgtgccattcgactgtggctcatgtacaatacgtttgaatttcacagGTTCGGAGTGTCTGGCTATCCTACCTTGAAATTTTTTCCCAAGAACAACAAAGACGGTGAAGATTATGATGGCGGTCGTGATGTGGACGCATTTGTGACT

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|18040454|gb|BM308748.1|BM308748
EST:     GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAAGTTTT-CCCAAAGAGCAAC
genomic: GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... tccaatacagATATGGTGTTAGTGGCTATCCTACACTGAA-GTTTTTCCCAAAGAGCAAC
EST: gi|192297309|gb|FG992403.1|FG992403
EST:     GTAGTTATGGCCAATGTTGATGCTGACA-GTATAAAGATT-GGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTT-CCCAA-GAGCA
genomic: GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... tccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCA
EST: gi|193361362|gb|FK325194.1|FK325194
EST:     GTAGTTATGGCCAATGTTGATGCTGACAAGTATGAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... tccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|192297310|gb|FG992404.1|FG992404
EST:     GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... tccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|193461347|gb|FK429292.1|FK429292
EST:     GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCT
genomic: GTAGTTATGGCCAATGTTGATGCTGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... tccaatacagATATGGTGTTAGTGGCTATCCT
EST: gi|58023280|gb|CX710021.1|CX710021
EST:     GATGCTGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GATGCTGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... tccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA
                           gcctaat  putative branch site (score: 3)
 ttttcc  putative PPT
 taatttagaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG