Sequence
atgc intronic sequence ATGC exonic sequence...aatcacttaagagctttttcaatgtcctatagattcattaaattttgaaataaattttgtccaagtcttctgatatgccactgttaccccttaattgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
Basic information
species | Glycine max |
transcript | GLYMA18G27710.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
aatcacttaagagctttttcaatgtcctatagattcattaaattttgaaataaattttgtccaa-------gtcttctgatatgccactgttaccccttaattgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
| | || | | | || |||| ||||||| | | ||| ||||| | |||| | || || | ||||||||| ||||| ||||| |||||||| ||||| || |||||||| |||||||| | | ||||| ||||| ||||||||||| | ||||||||||||||
--ttgtacttaaatttatctagaatactt---attctcaaaatttt--agttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 5
--aatcacttaagagctttttcaatgtccta-tagattcattaaattttgaaataaattttgtccaagtcttctgatatgccactgttaccccttaat-tgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
| | || | | ||| || || | | ||| || || | | ||| ||| || || | ||| | |||| | | |||||||||||||||| || | || || || ||||||||||| || || ||||||||| | | ||| ||||||||||||| |||||||||||||||||||||||
ccaggcgct---gtgttttctcttcttctttctcctttcctttttttcagcaggtaatagtgtgtcagctttgataaatgtt-taatcacccttggttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAAGCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
-aatcacttaagagctttttcaatgtcctatagattcattaaattttgaaataaattttgtccaagtcttctgatatgccactgttaccccttaat-tgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
| || ||| ||| | | | ||| || || | | ||| ||| || || | ||| | |||| || | |||||||||||||||| || | || || || ||||||||||| || || ||||||||| | | ||||||||||||||||| |||||||||||||||||||||||
ctgtgttttctcttcttcttctttctttc-tcctttcctttttttcagcatgtaatagtgtgtcagctttgataaatgtt-taatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaataaattttgtccaagtcttctgatatgccactgttaccccttaattgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
ttacccctt CT-rich tract
taaattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcacttaagagctttttcaatgtcctatagattcattaaattttgaaataaattttgtccaagtcttctgatatgccactgttaccccttaattgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - -caatgtc
- - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttacccc