Sequence
atgc intronic sequence ATGC exonic sequence...tcactgaattgatacttcaatcataatggatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
Basic information
species | Glycine max |
transcript | GLYMA07G38160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 3
---tcactgaattgatacttcaatcataatggatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
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aaaacatttgaccctaacatcaaa-gtgatagcctgaagttacttacattttatataagtgaagcttttaactgaaatgcatctttgtttataatcat--cagGTTTCAAGTAAAGAAAAAACAATTCTTCCGCAATTTTATGACAATTATTTTATTTGGTGCTGTGGGGACATTGATATCCTTTGTGATAATCTCTCTAG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 2
---tcactgaattgatacttcaatcataatggatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
|| | | | | ||| | | | | | ||||| || | | || ||| || || | | | | |||||| || || ||||||||||||||||||||||| || |||||||| | | | |||||||| |||| || | || || ||| | | || || || |
taatcttccagtaggaaattctgttacatcatttaaagtttaacattagt---cagcaaggtgaagcttactgttcctttttttctctttctttcctgagcagGTTCCAAGTTAAGAAGAAACAATTTTTCCGCAACTTCATGACTATTACGTTGTTTGGTGCGATTGGGACCCTAATCTCTTTCAGTGTAATTTCCCTCG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027851_T01 (Zea mays), 3'ss of exon 2
tcactgaattgatacttcaatc-ataatg--gatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
||||||| || |||| || | | || | || | | ||| || | |||| | | | || ||| | | || ||||||| ||||||||||||||||| || ||||| ||||| ||||| || | || || ||||| ||||| || ||||||| |||| || || || || |
-aactgaatgatctgttgaatccatgacgccaatcccttctagtt-tgatacttctttgacgtataatcaagattctcacagacgtttcctcacct-caccagGTTCCAGGTGAAGAAGAAACAGTTCTTCCGGAATTTCATGACAATCACACTATTCGGTGCTGTTGGCACAATGATATCCTTCTTCACAATCTCTCTCG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 3
tcactgaattgatacttcaatcataatggatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
| | ||| | ||| | |||| || || | || | | || || | | || ||| ||| |||| |||||||||||| |||||||| |||||||| ||||| || ||||| || ||| | |||||||| |||| ||| | || ||||| ||||| ||| | |
-------gtaagttcttt--ttatatagaatttcatg-aaaaattgaaagt------------cggaattgagt---aacacatttttt---tgttacagGTTTCAGGTTAAGAAGAAGCAATTTTTTCGCAACTTCATGACCATTATGTTATTTGGTGCTATTGGAACTCTCATTTCATTTGTTATCATCTCATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
ctgttcc CT-rich tract
ttcaatttcaatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactgaattgatacttcaatcataatggatttaatttaatgactgtgcttgcttctcttatactgacttcaatttcaatttattctttaactgttccagGTTTCAGGTGAAGAAGAAACAATTTTTCCGCAATTTTATGACTATAATGCTCTTTGGTGCAGTTGGTACTTTGATATCATTCTGCATCATATCACTAG
-cactgaa
- - - - - - - - - - - - - - - - - - - -atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgac