Sequence
atgc intronic sequence ATGC exonic sequence...ttcagttgctgtatgtcctccttaattccttatagtcttatacttctttaattgtcttggtatcctaattttaccgagatgcatctatttattgtgacagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
Basic information
species | Glycine max |
transcript | GLYMA15G00250.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G16710.2 (Arabidopsis thaliana), 3'ss of exon 7
---------ttcagttgctgtatgtcctccttaattcct-tatagtcttatacttctt-taattgtcttggtatcctaattttaccgaga----tg-catcta---tttattgtg---acagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
|| | || | | || | | | | || || |||| | | | | ||| | ||| | || || || ||| || |||| |||| ||||| ||| | |||||||| |||||||| ||||||||| |||||||||||||||| ||||| || || ||||| || || || || || ||||| ||| | |
gtttgctattttatttacaaaaagtttacagagaagcaagtctattcatatatctaagatgaatctctagctatgtgatcattgatgaataccttgtcatttaaattttaatgtgtgtgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGAATTCAATGAGTGAGAATTCCTGCCAGTTATGTGCGGTGGAGAAGCTTACATTTGAGCCACCAC
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 7
-ttcagt-tgctgtatgtcctccttaattccttatagtcttatacttctttaattgtcttggtatcctaattttaccga-gatgcatctatttattgtgacagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
| |||| || | || | | | ||| | | || ||| || || | | || |||| | | ||| || | | | ||||| ||| | |||||||| |||||||| |||||||||||||||||||||||||| ||||| ||| | ||||| || || || || || ||||| ||| | |
ctgcagtatgaggcttgattgagctgttccgttaaa--cacatttttccatattt-tatctaaatagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
upper sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 5
-ttcagttgctgtatgtcctccttaattccttatagtcttatacttctttaattgtcttggtatcctaattttaccgagatgcatctatttattgtgacagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
| |||| | | || || || || | |||| || | | | | | | | | | | ||| | || | ||||||| | || ||||| ||||||||||||||||||| ||| |||||||||||||| ||||| ||||||| || || || || ||||||||||| | |
tggctgttgagaatgatttttctgttttgtttttatttttattttttatgtactttgtctaggtttggtggtgattttttttcctct-tccctttttctagAGCAAGGCCAAGGCAGAAAAGAATCAAGCAATGGAGCGTTCGATGAGTGAGAACTCTTGTCAGCTGTGTGCAGTTGAGAAGCTTACTTTTGAACCTCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaattgtcttggtatcctaattttaccgagatgcatctatttattgtgacagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
tcctaat putative branch site (score: 2)
atctatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcagttgctgtatgtcctccttaattccttatagtcttatacttctttaattgtcttggtatcctaattttaccgagatgcatctatttattgtgacagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
- cagttgc
- - - - -tgtatgt
- - - - - - - - cctcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcat