Sequence
atgc intronic sequence ATGC exonic sequence...atggtagattaaaccccctagtatgttgtgtcagctaacattcttttgcatgtgatatttatccttcaggcacttacatttattatttttttaaatgcagCTACTACGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G16700.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------atggtagatt---aaaccccctagtatgttgtgtcagctaacattcttttgcatgtgatatttatccttcaggcacttacatttattatttttttaaatgcagCTACTACGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
|| || | | ||| | | ||| | || | | ||| | | | ||| | | | | |||| || || | | | | ||| || || |||||||| |||||||| |||||||| ||||||||||| ||||| | |||||||||||| |||| | | | |||||||||||| || |||
gtatcttttaagaacttagactatttagaatctcctcagtcctcaatggatgtttcaggtgctaaaattacaaaatgcagacaatgatactacaatggtcttcaattttttttttgtgcatatacctgaatc-cttattcttgtttgtctatgggtttcagTTATTATGATCCATACAGAGGTGTAATTGTATATTTTCGAGTTGTTGATGGCAGTATAAAGAAAGGGGACAAAATATGTTTTATGGCTAGCGGAAAG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 8
atggtagattaaaccccctagtatgttgtgtcagctaacattcttttgcatgtgatatttatccttcaggcactt-acatttatt-------atttttttaaatgcagCTACTACGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
| ||| | | || |||| || | | | | | || | ||||| | | |||| | |||| | ||| ||| ||||| || || ||||||||| | ||||| |||||||||||||||||| | ||||||| | |||||||| |||||| ||| ||| ||||| || || |||
-------gtgaaatactcgtgtttgttttgcttgatta-gtctacaagtgtgcagtttttatatgtgaactactttatatttttcgtccaaaattcattttgctgcagTTATTATGATCCATATCGTGGTGTCATTGTATACTTTCGAGTTATCGATGGGAAAGTGAAGAAAGGCGACAGAATTTTTTTCATGGCAAGCGGAAAG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 8
atggtagattaaaccccctagtatgttg-tgtcagctaacattcttttgcatgtgatatttatccttcaggcacttacatttattatttttttaaa----tgcagCTACTACGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
| | | | | | ||| || | ||||| | | | || | | || || || || | ||| |||| || ||| | ||| ||||| |||||||||||||| || || ||||| |||||||| | |||||||||||||||||||||||||| |||||||||||||||| ||||
-ttcttttgttttctctttgctattttaatttcagcatataacatattagcc----tttgcattatttgggtgtgtataaatatcatttcttcaaaccttttcagTTACTATGATCCATATAGAGGAGTGATCGTATATTTTCGAGTCATTGATGGGACTATAAAGAAAGGTGACAGGATTTATTTTATGGCTAGCAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcatgtgatatttatccttcaggcacttacatttattatttttttaaatgcagCTACTACGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
cacttac putative branch site (score: 2)
tttattattttttt CT-rich tract
acttacatttattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtagattaaaccccctagtatgttgtgtcagctaacattcttttgcatgtgatatttatccttcaggcacttacatttattatttttttaaatgcagCTACTACGATCCATATAGAGGTGTTATTGTATACTTTCGAGTTGTAGATGGGACTATAAAGAAAGGTGACAGAGTTTATTTTATGGCTAGTGGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - -cccccta
- - - - - - - - - - - -tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttac