Sequence
atgc intronic sequence ATGC exonic sequencegttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaattattatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
Basic information
species | Glycine max |
transcript | GLYMA01G44670.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 3'ss of exon 6
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatg-ggtatt-aatta--ttatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
||| | |||| | | | | || |||||| ||| | || || | | |||||||| || || || || || ||||||||||| ||||| |||||||||||||| ||||| || |||||||| || |||||||| |||||||| ||||||
-gtaggcgctttttgctggatagtctgtactacttctagccctcatttccatttatgtggtgctgaaatacttcaataaattgcagGAAGATCCTAACAACACTCCAGCTTCAGCTCGACATAAGAGAGGATGCAATTGCAAGAAGTCAAGCTGTCTTAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G153754_T01 (Zea mays), 3'ss of exon 6
--------------------gttagaaaataaacttgacttagtttttcacgtaagcaattgaaacc--accttttatgggtattaattattatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
||| || | | | || || | || || ||| | || | | || || || || | |||||| || || || || || || ||||| || || ||||||||||||||||| || || || |||||||| || |||||||| |||||||| || |||
gtatggcgttgcgtacttctgttggagattga----gatgtatgtacgtgtgttggccatttactcccagaccgtggtgcttacattctacaatgaaatcgcagGAAGATCCTAACAACACTCCGGCTTCGGCTCGTCACAAGAGAGGATGCAATTGTAAGAAGTCAAGCTGTCTCAAGAAATACTGTGAATGCTACCAG
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaat--tattatctt--tttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| || | | | ||| | || | | | | || |||| |||| | | |||||||| ||| ||||| |||||||| || || || || | || ||||||||||| ||||||| ||| || |||||||| |||||||| ||||||
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccacctttt--------atgggtattaattattatctt--tttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
| || | || | | ||| || || | || || | | | || ||| || | | || || ||||| || ||| |||||| ||||||||||| |||||||| |||| || |||||||| ||||||| ||| || |||||||| |||||||| ||||||
----gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtatta-attattatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
|| | | | | || | | | ||| | || || | || ||||||| |||||||| | | |||||| || ||||| ||||||||||| | || ||||||||||| ||||||| ||| | |||||||| |||||||| ||||||
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgc-acagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG
upper sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 7
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaattattatctttt--tgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
||||| | |||| | | | || ||| | | ||| ||| | ||| | |||| | | || | |||||||||| || | ||||| |||||||||||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||| ||||| ||||||
gttaggacataattcttgccttgtgttt-atacagaaaatctgaactgctagttaccc-tgttaagtgaggttttctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAACTGCAAGAAATCAAGTTGCCTAAAGAAATATTGCGAATGCTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacgtaagcaattgaaaccaccttttatgggtattaattattatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
tattaat putative branch site (score: 2)
ttatcttttt putative PPT
ttttatgggtattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaattattatctttttgcagGATGACCCAAATAAAACACCAGCTTCAGCACGACACAAGAGAGGATGCAACTGCAAAAAATCAAGCTGCCTAAAGAAATATTGTGAATGTTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA