Sequence
atgc intronic sequence ATGC exonic sequence...agttgcatgttgttagtatgttttgaattttgatttttttgttgagccaatttttacaaagttatctgacattctgtatatattcctccatctattgcagTTCTCTTGGTCAGAACCTTGCAACAAGTACCTATGTTTGGGAAATCAGCTTTGCTATTTTCATTTCAATTGCTGGTCTGGTGTTATTTGCATTCCTCATT
Basic information
species | Glycine max |
transcript | GLYMA06G13200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53130.1 (Arabidopsis thaliana), 3'ss of exon 5
--agttgcatgttgttagtatgttttgaattttgatttttttgttgagccaatttttacaaagttatctgacattctgtatatattcctccatctattgcagTTCTCTTGGTCAGAACCTTGCAACAAGTACCTATGTTTGGGAAATCAGCTTTGCTATTTTCATTTCAATTGCTGGTCTGGTGTTATTTGCATTCCTCATT
| | | || | || | ||| | | || || || || | ||| ||| ||| ||| | | | || | | |||||| || |||||||||||| ||||||||| ||| ||||||||||| | || || | |||||||| ||||| || ||||| || || | ||| | |||
gtattgagaatttatcagcaaaatttt--ctccgtttcttatgaagaaa-agtttcaacactaagttcttgcatctttgttctgttttcg----tgatccagTTCGCTCGGTCAGAACCTTAAAACAAGTACATATATTTGGGAAATCTGTTTCGCGGTGTTCATTTCTATTGCGGGGCTGGTTTTGTTCTCCTTCTTGATT
upper sequence: GLYMA06G13200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02560.t01 (Vitis vinifera), 3'ss of exon 5
-agttgcatgttgttagtatgttttgaattttgatttttttg--ttgagc-caatttttacaaagttatctgacattctgtatatattcctccatctattgcagTTCTCTTGGTCAGAACCTTGCAACAAGTACCTATGTTTGGGAAATCAGCTTTGCTATTTTCATTTCAATTGCTGGTCTGGTGTTATTTGCATTCCTCATT
| | || || ||| | | ||||| |||| || |||||| |||| | | | | || ||| | || || | ||| | |||||||||||||||||| ||||| |||||| |||||||| |||||||| ||||||| | |||||||| || |||| |||| |||||| |||| || |||
tctctttgtaatgataa-atgcatacacttttggttttcttactttgagcatcatttgtgtttattattgtggtattttatac---ttggtacattttttgcagTTCTCTTGGTCAAAACCTCAAAACAAGCACCTATGTCTGGGAAATTTGCTTTGCAGTGTTCATTTCCATCTCTGGCTTGGTTTTATTTTCATTTCTTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccaatttttacaaagttatctgacattctgtatatattcctccatctattgcagTTCTCTTGGTCAGAACCTTGCAACAAGTACCTATGTTTGGGAAATCAGCTTTGCTATTTTCATTTCAATTGCTGGTCTGGTGTTATTTGCATTCCTCATT
atctgac putative branch site (score: 3)
ttcctccatctatt putative PPT
tttttacaaagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttgcatgttgttagtatgttttgaattttgatttttttgttgagccaatttttacaaagttatctgacattctgtatatattcctccatctattgcagTTCTCTTGGTCAGAACCTTGCAACAAGTACCTATGTTTGGGAAATCAGCTTTGCTATTTTCATTTCAATTGCTGGTCTGGTGTTATTTGCATTCCTCATT
- - gcatgtt
- - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - -tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacattc