Sequence
atgc intronic sequence ATGC exonic sequence...agttttcaaaaacgaagctgtgatcttgttgaattaccaatgatcatatgcattgactatgctgcaactacatctgaattctgacaattcatgcaatcagATTATTAGGTTGGTGGTCAATTGATGAAGGGAGTCGGGAAGAACATGCACGACTATACCATGAGGGAGCAATTGG
Basic information
species | Glycine max |
transcript | GLYMA05G07960.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G73950.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------------------agttttcaaaaacgaagctgtgatcttgttgaattaccaatgatcatatgcattgactatgctgcaact-acatctgaattctga--caattcatgc--aatcagATTATTAGGTTGGTGGTCAATTGATGAAGGGAGTCGGGAAGAACATGCACGACTATACCATGAGGGAGCAATTGG
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gtgataattatgtttagttacttcctgatctgtttttaatgcgtatggaggctaaccataaaatatattttggtagctgcaaccgagt-tactaacaaacatcaagttgatgcctgacatttgatcctatacgtgctcgcttagGCTACTAGGTTGGTGGTCAATTGATGAAGGAAGCCGGGAGGAGGAAGCTCGACTATACTTTGATCAAGAATCTGG
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G18470.1 (Arabidopsis thaliana), 3'ss of exon 9
agttttcaaaaacgaagctgtgatcttgttgaattaccaatgatcata-tgcattgactatgctgcaactacatctgaattctgacaattcatgcaatcagATTATTAGGTTGGTGGTCAATTGATGAAGGGAGTCGGGAAGAACATGCACGACTATACCATGAGGGAGCAATTGG
|| || || | || || |||| | || | | | | | | | | | | | || ||||||| |||| |||||||||||||||||||||| ||||| || ||||| ||||| || ||||| ||| ||| || | |||
--------gtgacaaacacgtctgtctatt---ttcccaaaagttttaatttacaaaatgtagtactaacaaaaaatcaatcaatcaattcacttgttcagGCTATTAGGTTGGTGGTCAATTGACGAAGGAAGCCGGGAGGAACAAGCTCGACTGTACTTTGATCAAGAATCTGG
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------agttttcaa--aaacgaagctgtgatcttgttgaatt--accaatgatcatatgcattgactatgctgcaactacatctgaattctgacaattcatgcaatcagATTATTAGGTTGGTGGTCAATTGATGAAGGGAGTCGGGAAGAACATGCACGACTATACCATGAGGGAGCAATTGG
| ||||| | | | || | ||| ||| |||| ||| | | ||| || | || | ||| ||| |||||||| | | |||| | | ||||||||||| ||||||||||| ||||| |||||||| |||||||| |||||| || |||
gtaatgacttctacttcccaccagtaggaaatttcaggcaggcaagatggttaacttaaacaatgtaaccattgaatgtgttgtgcaactgtgaagtaattcttgctgcattttgacaatttctcaattcagGCTCCTGGGTTGGTGGTCCATTGATGAAGGAAGTCGTGAAGAACAGGCACGACTTGTCCATGATGGGGCAGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgcattgactatgctgcaactacatctgaattctgacaattcatgcaatcagATTATTAGGTTGGTGGTCAATTGATGAAGGGAGTCGGGAAGAACATGCACGACTATACCATGAGGGAGCAATTGG
ttctgac putative branch site (score: 2)
aattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttttcaaaaacgaagctgtgatcttgttgaattaccaatgatcatatgcattgactatgctgcaactacatctgaattctgacaattcatgcaatcagATTATTAGGTTGGTGGTCAATTGATGAAGGGAGTCGGGAAGAACATGCACGACTATACCATGAGGGAGCAATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - caaaaac
- - - - - - -gaagctg
- - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - ccaatga
- - - - - - - - - - - - - - - - - - - - - - - tatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac