Sequence
atgc intronic sequence ATGC exonic sequencegtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgtcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
Basic information
species | Glycine max |
transcript | GLYMA13G43770.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgtcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
||| | | ||||| | || | || || || |||| | ||| || | | |||||||||||||||||| ||||||||||| ||||| || ||||| ||||| || || || ||||||| || || ||||||||||| || || || ||||||
--gtaaatacaaatattttttgt--gtggataagatgctcccttga-tcttgttg----ctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgt----catgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
|||| || ||| || |||| | ||| || | ||| |||||| | ||||||||||| || | ||| ||||| || || || || ||||||||||||||||| ||||| |||||||| || ||||| || ||||||| |||| || |||
------gtacacgccttcgacttcatccgctattatgtcccaatgaggaactgaa-attctaacactcatgtttttcttgcagGTTATGCATAGCGTTCCTTACTTTCAGTTGCATTGGATATGCAATGCCATTCATACTATGTGCAACCATATGTTGTTGTTTGCCTTGCTTAATCTCGGTT
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 3
---gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgg-gcttcatg----tcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
|| |||| ||| | | || | |||| | || | | | || | || | | || || || ||||||||||| || ||||| || |||||||||||||| || ||||| |||||||| ||||| |||||||| || ||||||||| |||||||||||||||| ||
gtaatagttgtagttatgtatatagtccatttctattagaattccaccccttttgagccactcaagtgtctcttgcccttcctgcagGTTATGCATAGTGTTCCTCACCTTTAGCTGTATTGGCTATGCTATGCCATTCATACTATGTGCAACAATCTGTTGCTGCTTGCCTTGTATAATTTCAATT
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S74_109V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgtcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
| | || |||| | || | || | ||| | || | | | |||||||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||| ||||| || |||||||| |||||| |||| || |||||| | |
gtaggtgacgcagtgtggtgttgtgggaaggttggttggttgtggcggtggcctgtgaattgtggtgtgggtcggagatggtagtgaagttgcaaaggttgtggggagaagaatggacagtaagagggttgtgagtggggttttg-gcagGTTATGCATCGTGTTGCTTACGTTCAGCTGCATCGGATATGCGATGCCTTTTATTCTTTGCGCCACTATTTGCTGCTGCTTGCCGTGCATAATTGCACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccagtattttactttctcgagtcttcgagtaatctgggcttcatgtcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
tattttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgtcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC