Sequence
atgc intronic sequence ATGC exonic sequence...taaccaatgtttggattgaatgcctgactgactaactgattcaattgctatattctgtggatattgatatcagtaattaatctaacacatgtttctacagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
Basic information
species | Glycine max |
transcript | GLYMA20G22300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G22300.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------taaccaatgtttggattgaatgcctgactgactaactgattcaattgctatattctgtggatattgatatcagtaattaatctaacaca-tgtttctacagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
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gtaaagttctcttctttcatgtcttcgcttttatatatgttgcttagaacacccactatttctcttgcttacggaaacattg-ctaaacatttacttatggtaataactcaaa-acaaaactgcatgcct-tagaccttatctgttttggtgttttggtgtttgggcagTTTGGGGAGCCTGCAACCACGCGTTTCATCTTCACTGTATATTGAAATGGGTGAATTCGCAGACGAGCCAAGCTCATTGCCCAATGTGCAGAAGAGAATG
upper sequence: GLYMA20G22300.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g03770.t01 (Vitis vinifera), 3'ss of exon 2
taaccaatgtttggattgaatgcctgactgactaactgattcaattgctatattctgtggatattgatatcagtaattaatcta---acacatgttt----ctacagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
| | | || || || | | || || | || | | | | ||| || | |||| | |||| || ||||| || |||||||||||| ||||| || ||||||||||| || || ||| |||||||||||||||| ||||| | ||||||||||||||||||||||||||||| ||
------ttatatatat-aaaaaaaagattaaagaaacttttaagttttttttaggaattggtatcaatccaactaatgattctattaaccattgttttgtcctgcagTTTGGGGTGCTTGCAACCATGCATTTCATCTCCATTGCATCTTGAAATGGGTGAATTCGCAGACTCCTCAAGCGCATTGCCCCATGTGCCGTAGGGAATG
upper sequence: GLYMA20G22300.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g00290.t01 (Vitis vinifera), 3'ss of exon 5
taaccaatgtttggattgaatgcctgactgactaactgattcaattgctatattctgtggatattgatatcagtaattaatcta---acacatgttt----ctacagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
| | | || || || | | || || | || | | | | | ||| || | |||| | |||| || ||||| || |||||||||||| ||||| || ||||| ||||| || || ||| |||||||||||||||| ||||| | ||||||||||||||||||||||||||||| ||
------ttatatatat-aaaaaaaagattaaagaaacttttaagtttttttttggaattggtatcaatccaactaatgattctattaaccattgttttgtcctgcagTTTGGGGTGCTTGCAACCATGCATTCCATCTCCATTGCATCTTGAAATGGGTGAATTCGCAGACTCCTCAAGCGCATTGCCCCATGTGCCGTAGGGAATG
upper sequence: GLYMA20G22300.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S46_78V6.1 (Physcomitrella patens), 3'ss of exon 2
taaccaatgtttggattgaatgcctgactgactaactgattcaattgctatattctgtggatattgatatcagtaattaatctaacacatgtttct------acagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
| | ||| | | | | | | ||| || | | |||| | | || | | | |||| ||||| | | |||| ||||| | ||| ||||||||||| ||||||||||| ||| |||| |||||||| || |||| | | | || ||||| ||||| ||| |||| ||
-----attatttttttcttctccttttgctgtagagaaagccaactgttctcttcttcaca-actgggtttgaccaggatgctaatacatgatgtttgcttggcagTGTGGGGAGCATGTAATCACGCATTCCATCTGCACTGCATCTTGAAGTGGGTGAACTCCCAGAGCCCGCGGCCTCAGTGCCCAATGTGTCGTCGGGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctatattctgtggatattgatatcagtaattaatctaacacatgtttctacagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
atctaac putative branch site (score: 2)
tgtttct putative PPT
atattgatatcagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaccaatgtttggattgaatgcctgactgactaactgattcaattgctatattctgtggatattgatatcagtaattaatctaacacatgtttctacagTTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTAGGGAGTG
- -ccaatgt
- - - - - - - - -gaatgcc
- - - - - - - - - - - - - -ctgacta
- - - - - - - - - - - - - - - - - - - - -caattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat