Sequence
atgc intronic sequence ATGC exonic sequence...caaatgaatagtgtaacctattctttactattatttactttcttcttgtttgctatttgatttgatttcttacatgtatttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
Basic information
species | Glycine max |
transcript | GLYMA06G11120.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 8
caaatgaatagtgtaacctattctttactattatttact-ttcttcttgtttgctatttgatttgatttcttacatgtatttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
| ||| | || || ||| || | ||| |||| ||| | | || | | ||| | | | | | | |||| |||||||||| || |||||||| | |||||||||||||| |||||| ||||| |||||||||| ||| |||| ||||||||||||||| ||||| |||||
-----gtataatctacgtccttatttcttacaggcagcggttcctcttctttatccatgcacacgaataatgtactgtctgtt-tctctttaatttcgtagAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATC
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 8
caaatgaatagtgtaacctattctttactattatttactttcttcttgtttgctatttgatttgatttcttacatgtatttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
|| | || | | | ||| || || | ||||| || || | ||| | |||| | | ||| ||||||||||| || || || || |||||||||||||||| |||||| ||||||| |||||||| ||| |||| | |||||||||||||| |||| ||||
----------gtatggtcttgcatcctggggcagtggttttttttttctaggctatatgcttatgtaatgtac---tgtttcgc---ttttgtttgatagAGATAAGACGGTTTTACGGTATGGAACATGGTGGAGGATATGATTCTTGGAGGAAAACATCGGTTGTAGCCTCTCCTTTTGATTTTGATGAAGCTGAATC
upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 8
-caaatgaatagtgtaacctattctttactattatttactttcttcttgtttgctatttgatttg-atttcttacatgt----atttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
| || | ||| ||| ||| | | || | || || ||| | || | | | ||| | || | || || |||||| |||||| | |||||||| |||||||||| ||||| |||||||||||||| | |||||| ||| | ||||||||||||||||||||||||||| | ||
gtatgctcttatcgatcttcatttttttctag-acctttttctcagtctttcacttcttgttatgtgtatgctgcatctgactatattattgactgtcttaaatagAAATAAGGAGATTCTATGGAATGGAACATGGCGGAGGATATGATGCTTGGAGGAGAACATCAGTTGTTGCTACCCCTTTTGATTTTGACAAAGCAGAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttgctatttgatttgatttcttacatgtatttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
ttcttac putative branch site (score: 2)
tctcattt putative PPT
tatttgatttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaatgaatagtgtaacctattctttactattatttactttcttcttgtttgctatttgatttgatttcttacatgtatttcatgtgtctcatttaatagAGATAAGGCGTTTCTATGGGGTGGAACATGGTGGAGGGTATGATGCTTGGAGAAAAACATCCGTTTTAGCTACCCCTTTTGATTTTGACAAAGCACAATC
- - - - - -tgtaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtg