Sequence
atgc intronic sequence ATGC exonic sequence...agcttttgcattgtgactcctattacaatatcgaggatcatatttttccgtgtttttcctattgacatttcttgtttacttgggatttttgtgtgatcagGTCAAAGGTGAAGCTAATATATCACATATATGTTCACTTTTCTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTT
Basic information
species | Glycine max |
transcript | GLYMA05G29200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G29200.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 5
---agcttttgcattgtg-actcctattacaatatcgaggatcatatttttccgtgtttttcctattgacatttcttgtttacttgggatttttgtgtgatcagGTCAAAGGTGAAGCTAATATATCACATATATGTTCACTTTTCTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTT
|| |||| | | | ||| | | | | | ||||| ||| | || ||| || || ||||||| | || ||||| ||||||||||| || || || | || || |||| |||||||| ||||| || || || ||||||||||||||||| || ||||| |||||||| |
gtaagactttgtgacatataaactcattcgacttgtagcggttgttgttttctgtgatcttgtcatttactgttgaaatttacttttgctt----------cagGTTAAAGGTGAAGCCAACATTTCTTACATCTGCTCACGATTCTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCT
upper sequence: GLYMA05G29200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 6
agcttttgcattgtgactcctattacaatatcgaggatcatatttttccgtgtttttcctat-tgacatttcttgt----ttacttgggatttttgtgtgatcagGTCAAAGGTGAAGCTAATATATCACATATATGTTCACTTTTCTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTT
| || ||| || || | || || || || | ||| || |||| | | ||| || | | | | || | || | | ||||||| ||||||||||| || |||||| | |||||||| | ||||||||| ||||| ||||| || ||||| ||||| |||||||| || ||||||||||| |
---tctttcatggtagtcagtact-cagtag-gaagaaagtctttgcttgttttttctttctatgatatctttcatgttttcaccatgaatccaattttcatcagGTTAAAGGTGAAGCAAACATATCATACATATGTTCTCGTTTCTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccgtgtttttcctattgacatttcttgtttacttgggatttttgtgtgatcagGTCAAAGGTGAAGCTAATATATCACATATATGTTCACTTTTCTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTT
tattgac putative branch site (score: 2)
tttttgt putative PPT
atttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcttttgcattgtgactcctattacaatatcgaggatcatatttttccgtgtttttcctattgacatttcttgtttacttgggatttttgtgtgatcagGTCAAAGGTGAAGCTAATATATCACATATATGTTCACTTTTCTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTT
-gcttttg