Sequence
atgc intronic sequence ATGC exonic sequence...tttgtggtcatgctgcattactaatctaacaatctattctaaattctaaataagatgtatttttccacttttaaatcatggatgatccccttgtctttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
Basic information
species | Glycine max |
transcript | GLYMA14G38800.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os06g03770.1 (Oryza sativa), 3'ss of exon 18
tttgtggtcatgctgcattactaatctaacaatc-tattctaaattctaaataagatgtatttttccactt--ttaaatcatggatgatccccttgtctttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
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-ctg-aattatttcacactgttaa-caaacactaattttgcaaaagatgagtttactgcattcctccctttgcttattttttttgttatctaatttataccagATTGTGTGATGAAGCTACAAGCGCTCTTGATAGCACCACCGAAGCGTCAATTTTAAATTCTCTGAAGACTTTGTCCGTTGACCGTACCTCTATCTTTATT
upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G032936_T01 (Zea mays), 3'ss of exon 13
tttgtggtcatgctgcattactaatctaacaatctattctaaattctaaataagatgtatttttc-cacttttaaatcatggatgatccccttgtct--ttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
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-caggactagtttcaaattact--tgcaggaagttttttttgtgtgcaaatagtaggcttatccaatgcccgtttgtcttgacttttttctttactatgtcagGTTATGTGATGAAGCAACTAGTGCTCTTGACAGCACTACTGAAGCATCAATTTTGAATTCTCTGAAATCCTTATCTTCCGATCGAACATCAATCTTTATT
upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G58270.1 (Arabidopsis thaliana), 3'ss of exon 16
tttgtg-gtcatgctgcattactaatctaacaatctattctaaattctaaataagatgtatttttccacttttaaatcatggatgatccccttgtctttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
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---gtaagtaactttgca---cagaagcagca-ttgagtttacttatgtgattatgtacgtgtctagtcctcacatacatagagatggttggtgtacacagGTTGTGTGATGAGGCAACGAGTGCGCTGGACAGCACAACAGAGGCAGAGATACTGAACGCACTCAAGGCACTAGCGAGTAACAGGACATCTATCTTCATT
upper sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv06s0004g08350.t01 (Vitis vinifera), 3'ss of exon 20
tttgtggtcatgctgcattactaatctaacaatctattctaaattctaaataagatgtatttttccacttttaaatcatggatgatcc----------ccttgtctttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
||| | | | | | | || || | || | |||| | | | || || | || || ||||| | | | | | || | |||||||||||||| ||||| || |||||||||||||| ||||||| |||| |||| | ||| || ||||||||||||| ||||| || || ||
----tggaaaggggaggatgttc-tgtcaccattttttttttcttcttttt-----ctttccttttcctctcaagcagtgtatgattctaatctcaatctgtcccctcagACTTTGTGATGAAGCTACGAGTGCACTAGACAGCACAACAGAGTCAGAGATATTAAATGCACTGAAGACATTAGCAAATAATCGAACTTCAATCTTTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaataagatgtatttttccacttttaaatcatggatgatccccttgtctttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
ttctaaa putative branch site (score: 2)
tccccttgtcttt putative PPT
taagatgtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtggtcatgctgcattactaatctaacaatctattctaaattctaaataagatgtatttttccacttttaaatcatggatgatccccttgtctttagGTTGTGTGATGAAGCTACAAGTGCTCTTGACAGCACAACAGAAGCAGAGATTTTAAGTGCATTAAAGTCAGTAGCAAATAATCGGACTTCCATATTCATT
- - - -tcatgct
- - - - - - - gcattac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatcccc