Sequence
atgc intronic sequence ATGC exonic sequence...gtttttttccttaaatatccatgtttcttatagtcaaactgacaatggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
Basic information
species | Glycine max |
transcript | GLYMA04G33480.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 12
gtttttttccttaaatatccatgtttcttatagtcaaactgacaatg---gtggggttagtga---ttaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
| | || | | ||||| || | | || | || || | | || | | || || | |||| | ||| | ||||||||||| || | || ||||||||||| |||||||| | |||||| ||||| || |||||||||||||| ||||| |||
----agatgccaaattgccaatgttgattggtgactaattagcattgtgcattgcatttctcatctttgcttttctaaaggcagtaacaaggttttcaat--gcagTTTGAACCAGAATCTTCAAGTGCCATGGGTTTTGGCTTCAGATGTGGATTTCTCGGTCTTCTTCATATGGAGATTGTGCAG
upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G003157_T02 (Zea mays), 3'ss of exon 3
-gtttttttccttaaatatccatgtttcttatagtcaaactgacaatggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
| | | | || | | | | | || | || ||| || || | || |||| | | | | | ||||||||||| || | || ||||||||||| |||||||| | ||||||||| || || ||||| ||||||||||| ||||||
tgcatctgttctcatttggattctgtaatattggttattctttatgcattggtattt-tgtatgatacttcattttctctaaatccatgccattaatgcagTTTGAACCAGAATCTTCTAGTGCCATGGGGTTTGGCTTCAGATGTGGGTTCCTTGGTCTTCTCCATATGGAAATAGTTCAG
upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
--gtttttttccttaaa-tatccatgtttcttatagtcaaactgacaatggtggggttagtg-attaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| | ||| | ||| ||| || ||| | || | | | | | | ||| || || | | ||| | ||| | | |||||||| ||||| || ||||||||||||||||||||||||| ||| |||||| |||| ||||| || ||||||||||| |||
atgtatctttgttaaaaatattcacatttggtctaa--ggagcgtatacgttagcattaacatatctataggtt--tgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG
upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 12
--gtttttttccttaaatatccatgtttcttatagtcaaactgacaatggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| ||| | |||| || || || | | || | || ||| | ||| | | | | || ||| |||||||| ||||||||||| ||||||||||| |||||||||| |||||||| |||| ||||| ||||||||||| |||||
ctattgtttggttgtaataagggcgtagttt-taatggtatatgcagatcttgg-ttacttgctaaagaattgtgctcccttcttcaatgtccattttgcagTTTGAGCCTGAGACATCCAGTGCCATGGGCTTTGGCTTTAGGTGTGGGTTCTTGGGTCTTCTCCATATGGAAATCATTCAG
upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 12
gtttttttccttaaatatccatgtttcttatagtcaaactgacaatggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| | | ||| | | | | | |||| || ||| |||| | | | | | ||||||||||| || | |||||||| ||||||||||| ||| |||||| ||||| |||||| | || |||||||| || |||
--------------------------------gtatggcct-cgatgctaag--tcgccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG
upper sequence: GLYMA04G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 12
gtttttttccttaaatatccatgtttcttatagtcaaactgacaatggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
|| | | ||| | | | | |||| || ||| |||| | | | | | ||||||||||| || | |||||||| ||||||||||| ||| |||||| ||||| |||||| | || |||||||| || |||
--------------------------------gtatggcct-cgatgctaagcc--gccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
gattaat putative branch site (score: 3)
tttcattcttttttct putative PPT
attaattattcaaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttttccttaaatatccatgtttcttatagtcaaactgacaatggtggggttagtgattaattattcaaagatttcattcttttttctggtttacagTTTGAACCTGAGACATCGAGTGCCATGGGATTTGGCTTTATATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
- - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - -actgaca
- - - - - - - - - - - - - - - - - - - - - - -tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - gttagtg