Sequence
atgc intronic sequence ATGC exonic sequence...agttatttttcctatgtaaacattcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
Basic information
species | Glycine max |
transcript | GLYMA18G04580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g33150.1 (Oryza sativa), 3'ss of exon 2
---------agttatttttcctatgtaaacattcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgc-agaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
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gtacgataacattgtcctcgacacgttgggacaacatgcctgaacgtatgat--aaattagttttttaatgtatatataac---catttttatatacaaaacatgttagGTGGTCTAAGATTGCGTCTCATTTGCCTGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACTCACATCAAGAAGAAGCTCAAGAAAATGGGGATC-
upper sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 2
agttatttttcctatgtaaacat-tcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
|| | | ||| || || | || | | | | || | | | | ||| | | | | | ||||||||| |||||||| | | ||||| || || || || || ||||||||||| |||||||| |||||||| ||||| ||||||||||| ||||| ||
-gtgacaatgcctccaaaatcagatgctgccgcatgcatgccgcc--actcgatccaaaatctcatgg--tgtttttgtgcgtcgcgtgcgtgcgtacagATGGTCCAAGATTGCGGCACGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAAGAAGATGGGCCTT-
upper sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
agttatttttcctatgtaaacattcctagtatggacct-tttgttggaatc--atttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
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--tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT-
upper sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 3'ss of exon 2
---agttatttttcctatgtaaacattcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
|| |||| | || || | | | | | | | | || ||| || || |||| | || ||| ||| | ||||||||||| ||||||||||||||||| ||||||||||||||||| || |||||||| || |||||||||||||| |||||||| || || || ||||| |||
ttccttttttttgtccctgaaattaattccaaaacatatccatg--tgaaattcttcttcaattttaatttatatgtttgttttttcaacgtggatttgcagATGGTCCAAGATTGCTTCTCATCTACCAGGAAGAACCGATAACGAAATCAAGAACCATTGGAATACCCACATCAAGAAAAAACTTAAAAAGATGGGTATT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatcatttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
tactaat putative branch site (score: 1)
tgtcctttttttcccc putative PPT
atttttttcctttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttatttttcctatgtaaacattcctagtatggaccttttgttggaatcatttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - cctatgt
- - - - - - - - - - cattcct
- - - - - - - - - - - - - - - - - -ccttttg