Sequence
atgc intronic sequence ATGC exonic sequencegtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
Basic information
species | Glycine max |
transcript | GLYMA10G30930.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
gtagatatacta-tcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
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--------acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagatttttt---acattttttttccaaatgtgttaatttt--ctgatgcctaa-tgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
| || | | | | ||| | ||||||| | | | || | | | || | || || | | || || || | || || ||||| ||||| || |||||||| || ||||||||||| |||||||||||| |||| |||||||| || || || || || ||||| |||| ||||
---------ccatttgttttgtgtggattacatttgttcactgttttct--ttatatagtcttaactgtgtataacgtttactgagttaataatcttggatcatggt--gcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
gtagatatactatcattatcattaaattcacacaa-tgactctgtttttcagccaaa-atatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
| | ||| || | | ||| | | | |||| | | |||| | | | | ||| || | | | ||| |||||||| ||||||||||| ||||| ||||||||||| || |||||||||||||| |||||||||||| | || |||||||| |||||||| ||||||
-----------------------gtactgacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt-tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaa--aatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgt-agGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
| ||| || || | || ||| | | ||| | | ||||| | || | ||| | | ||||||||||| ||||| ||||| ||||| ||||||||||| || |||||| ||||||||||||| ||||||||||| |||||||||||||| ||| |||||
------------------------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactc-tgtttttcagccaaaat-atattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
| | ||| || | | || | | | | ||| | | |||| | | | | || | | | | ||| |||||||| ||||||||||| ||||| ||||||||||| || |||||||||||||| |||||||||||| | || |||||||| |||||||| |||||
-----------------------gtactgacaaaaatatttgcgtgctattgttgtatttatagtattgtttttgctcatttaacatcacttttctattcactt-tggcaattagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
||| | ||| ||| | | |||| | | || | |||| ||| | || | || | || | | || || |||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||| ||||||||||||| |||||||||||||| |||| | |||||
-----tatcagtttgccctcacgaaaagta-attatgataccacgacgtgagcttaagtttctgatcat---gtgcccttaggctaaatattgta----agcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
|| | ||| | | || | ||| | | | || | || || || ||| | | | || | | | || |||| | || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||| |||||||||| || || ||||||||||| | ||| | |||||
-------tattggcat-gccctcaatagaagacagt-atggtacattgatgtgaatttaggtttctacttgtgtatct---gtaggctca-tccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctg-tagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
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--------------------------------------------------------gtaagtcctattcgagatatccaatatgtttttgct------gacagtgggatactagATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 7
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctg-tagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
|| | | || || | ||||||| || | | | | || ||| || || || || || || ||||| ||||| |||||||| ||||||||||| || || || ||||| |||||||| ||||| | ||| | |||||
--------------------------------------------------------gtaagtcctattcgagatacaata--tgtttttgct------gacagtgggatgctagATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
acctaat putative branch site (score: 3)
tttttactttacctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA