Sequence
atgc intronic sequence ATGC exonic sequencegtagtaattgattagatgtaatccacctccatacattttaacctcaaggaatatttactaacataaatgctccttttttccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
Basic information
species | Glycine max |
transcript | GLYMA06G11860.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 8
gtagtaattgattagatgtaatccacctccatac-attttaacctcaaggaatatttacta--acataaatgct---ccttttt---------tccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
| | || | || || | || | ||||||| ||| || | | | | || | ||| ||||| | ||||| | ||||| ||||||||| | ||||||||||| | ||| |||||||| |||||| | ||||| || ||||| ||||||||||| ||||| ||| || || ||||
atcttttttcagta-atctgattgatctccatattattctagtcactattatctgttggcatcacaccgatgcttgacatttttgtaattatattatccagCTGATTGACTGGTCAGAAGGTGGATACTTAACAAGTGACTCCCCAATGCCTCGAGGAGAGATTGTCATTGGTGGTCCCAATGTAACTAAAGGCTATTTCA
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 3
-------gtagtaattgattagatgt---aatccacctccata-cattttaacctcaagg----aatatttactaacataaatgctccttttttccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
| || | | |||| || || || || ||| || || | | ||| ||||| ||| | || | | || | || || ||| | ||||||||||||| ||| | ||| ||||||||| | || |||||||| || ||||| |||||||| || || || ||||| |
gtttattttggttttctccttcatgttgagattcagaagattaatatcttatccctcagatcttattctttcctaacgtaa-tatgaattgtatatgatagTTGATAGATTGGGCTGAAGGTGGATATTTAACTAATGATTCACCAATGCCTCGGGGTGAAATAGTTATTGGAGGTCCAAACGTGACAAAAGGCTACTTTA
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 6
------------gtagtaattgatt---agatgtaatccacctccatacattttaacctcaaggaatatttactaacataaatgctccttttttccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
| | || ||| | | | | | ||| | ||| | | ||| ||| ||||||||| | | | || | || |||||| ||||||||||||| | ||| | || ||||||||| | || |||||||| || ||||| ||||||||||| ||| || |||||||
ttttattcgtatggtttctttcattttgtggtatgagttatttcccttggtttcagacgcaatattgttttcctaacataatttcaatcacgcattat-agTTGATAGACTGGGCCGAAGGTGGATACTTAACAACCGATTCACCAATGCCTCGGGGTGAAATAGTTATTGGAGGTCCAAATGTAACTAAAGGCTACTTCA
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 9
----------------gtagtaattgattagatgtaatccacctccatacattttaacctcaaggaatatt-tactaacataaatgctccttttttccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
|| | || ||| |||| || || ||| || || || || ||| |||| || | || | | |||| | || | ||||| || ||||| |||| ||| ||||| ||||||| | ||||| ||||| || ||||||||||||||||| ||| ||||||| ||||
cgagaaaatcttataccctgttgtaattttgat-taatgcatttcaatatatggccttactaattctaatcatattaagataa-tgttt-ttctctgtttcagTTGATAAATTGGCCTGAGGGTGGGTATTTAACAAGTGATAAACCAATGCCTCGAGGAGAAATAGTCATTGGTGGTCCAAATGTTACTGTTGGATATTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacattttaacctcaaggaatatttactaacataaatgctccttttttccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
tactaac putative branch site (score: 0)
tgctccttttttccct putative PPT
aatatttactaacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtaattgattagatgtaatccacctccatacattttaacctcaaggaatatttactaacataaatgctccttttttccctcagCTAATTGACTGGCCCGAAGGTGGATATTCAACCAGTGACTCACCAATGGCGCGAGGTGAAATTGTAATTGGTGGTCCAAATGTCACTCTTGGATACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG