Sequence
atgc intronic sequence ATGC exonic sequence...ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
Basic information
species | Glycine max |
transcript | GLYMA11G14100.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g01870.t01 (Vitis vinifera), 3'ss of exon 1
ttattcatgtatgtg-tgagtgtgtcaatggcttccaaattcttcatctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
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-tccccagttaccaactcaaagtttcatatataattgaatgtatggttttggttttgtatgagactaatttaacttgccttcaaaatacctcatgctgtagATGCATATGTGGGGGCATGGATCTCAGTATAGAAAAGGGCCAGAGTCTCTGAGGGGAACACAGCCAACGGCCATGCTTAAACTCCCATGCTTTTGCTGTG
upper sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S359_44V6.1 (Physcomitrella patens), 3'ss of exon 3
----ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatctaattattc-tatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
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tggatcagaagtccacagggatttgtttagattacctg-atagaatccaggtgataaaaagtggggccacac-ttacaatgaaccggatgtggga---tgtgtagATGCACATGTGGGGCCATGGATCCCAATATAGGAAAGGCCCTGAATCGCTTCGAGGAACCCAACCCACTGCCATGCTGAGGCTGGCATGCTACTGTTGCT
upper sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16937 (Selaginella moellendorffii), 3'ss of exon 1
-ttattcatg-tatgtgtgagtgtgtcaatggcttccaaattcttca--tctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
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gtcttccatgatcagagcatgcatttttctgaaaaaaaaatttaaaaaattatatgacttaaaaatctcaattttctcttacctgtgtgtga----ctgaacagATGCATATGTGGGGGCATGGATCCCAGTACCGCCGCGGCCCCGAGTCACTGCGCGGCACGCAGCCCACCGCAATGCTCCGGCTGCCCTGCTACTGCTGCG
upper sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ25578 (Selaginella moellendorffii), 3'ss of exon 1
ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
| |||| | ||| | | | | | | | || | | || | | ||| | ||||||||||||||||||||||| ||||| ||| || ||||||||| ||| | | || | || || ||||| |||||||| || || ||||| ||||| |
-------------------------gttcacttcttttcttttcttttgaa-actgcaagttcaagacaaacttttatgtcctt-tgtttctcttc-cagATGCATATGTGGGGGCATGGTTCTCAGTATCGGCGGGGACCAGAATCTTTGCGAGGTGCTCAGCCGACAGCCATGCTAAGGCTTCCATGCTACTGCTGCG
upper sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16056 (Selaginella moellendorffii), 3'ss of exon 1
--ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatcta---attattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
|||| || | | | | || || ||||| | | || || | | | ||| | | | | | ||| | || ||||||||||||||||||||||||||| || || | || || ||||| || | || || || || || |||||||| | || || ||||| ||||| |
atcagagcatgcatttttctgaa-gaaaaaaaatttaaaattatatacgtatccatgacttaaaaatctcatttttctcttacctgtgtgtga----ctgaacagATGCATATGTGGGGGCATGGATCCCAGTACCGCCGCGGCCCCGAGTCACTGCGCGGCACGCAGCCCACCGCAATGCTCCGGCTGCCCTGCTACTGCTGCG
upper sequence: GLYMA11G14100.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22315 (Selaginella moellendorffii), 3'ss of exon 1
ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
|| | ||| ||||| || || | | | | || | || | | | ||| | |||||||||||||||||||| || ||||| ||| || ||||||||||||| | | || | || || ||||| |||||||| || || ||||| ||||| |
----------------------gttcacttcttttcgtttctt--tcgaa--actgcaagttcaagacaaacttctatgtcgtt-tgtttctcttc-cagATGCATATGTGGGGGCACGGTTCTCAGTATCGGCGGGGACCAGAGTCTTTGCGAGGTGCTCAGCCGACAGCCATGCTAAGGCTTCCATGCTACTGCTGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
ctcttac putative branch site (score: 3)
tgataataatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattcatgtatgtgtgagtgtgtcaatggcttccaaattcttcatctaattattctatgctcttacgtgataataatattggtgcaaaaatctacacagATGCATATGTGGGGGCATGGATCTCAATATAGGAAGGGACCAGAGTCTCTAAGGGGAACACAACCAACAGCAATGCTAAGACTCCCTTGCTATTGCTGTG
- - -catgtat
- - - - - - - - gagtgtg
- - - - - - - - - - - - - - -gcttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgca