Sequence
atgc intronic sequence ATGC exonic sequencegttagtctcaaaactctacattatttgcccaaagcagagtagaattagaaaaggaaacagaatttgagcctgatggatttcaatctcaattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaatagGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
Basic information
species | Glycine max |
transcript | GLYMA13G43270.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43270.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G16260.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtctcaaaactctacattatttgcccaaagcagagtagaattagaaaaggaaacagaatttgagcctgatggatttcaatctcaattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaatagGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
||| | || || || || || | | |||| ||| || | || | | || ||| |||||| | |||||||||||| |||||||| |||| ||||| ||||||||||| |||| | ||||| ||||| |||||||| || ||| || | | | | ||| | |
--------------------------------------gtatgtctcaaagagcaatca---ttgggaatcttcacaacccaatatcagtttc-tatac----aagcagactaac---actgttcacgcttaatcatagGTTCATCCGAGTGATGTGATGGGACCTTCAGTTCCTGGTCCTGTTGTTTTGCTTGTGGATTGTCCAACAGAGTCACATGCCGAGGAACTGCTATCTATCC
upper sequence: GLYMA13G43270.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtctcaaaactctacattatttgcccaaagcagagtagaattagaaaaggaaacagaatttgagcctgatggatttcaatctc-aattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaat-agGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
| | | | | | ||| | || | |||| | | | || | | | ||||||| |||||| | | | | ||||||||||||||||||| |||| ||||| | |||||||||||||| |||||||| || || |||||||| || || | || | | || || |
-----------------------------------------------gtatacctgcgattaccaatgactgtttttttcctctctctgagtggagatattgtatgaaattgtaac-tgactgttcatgctttgatcttagGTTCATCCAAGTGATGTTATGGGACCTTCACTCCCTGGTCCCATTGTTCTCCTTGTGGACTGTCCAACAGAGTCGCACGCTGCAGAACTGTTCTCACTTA
upper sequence: GLYMA13G43270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 6
gttagtctcaaaactctacattatttgcccaaagcagagtagaattagaaaaggaaacagaatttgagcctgatggatttcaatctcaattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaatagGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
| ||| || |||| ||| || | || || | || | | | ||| ||||| ||| | |||||||||||||||||||| |||| |||||| |||||||||| ||||| | ||||| || |||||||| ||||| || | | | | || || ||
---------------------------------------------------------gtgggttta---cttatggtgttctatgtatgtttcataccatttgttttgatccatagct-ttgtttttcttattttttagGTTCATCCAAGTGATGTGATGGGACCTTCTATTCCTGGTCCTCTTGTATTGCTTGTAGACTGCCCAACGGAATCATATCTACAGGACCTTTTATCCGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcaattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaatagGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
tactaaa putative branch site (score: 1)
tactaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctcaaaactctacattatttgcccaaagcagagtagaattagaaaaggaaacagaatttgagcctgatggatttcaatctcaattacacatgcttcaatacattgtaaagcaactgtttgtctactaaaatagGTTCATCCAAGTGATGTCTTGGGTCCTTCTGTTCCTGGTCCCATTGTACTCCTTGTTGATTGCCCAACAGAATCTCATTTGGAAGCATTATTGTCTGTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG