Sequence
atgc intronic sequence ATGC exonic sequencegtaaattactcacatgacgagaaattattttatagaagctgtttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
Basic information
species | Glycine max |
transcript | GLYMA04G11550.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 11
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 13
---------------------gtaaattactcacatgacgag---aaattattttatagaagctgtttaa--aatgctgaattgacattagtaaaatatt-tgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
| ||| | |||| | | || | | || | | || | | ||| || | | || | || ||||||||||||| |||||||||||| || ||||| ||||||||||| | ||||| || ||||| ||| ||| |||||||| || |||||| | || || |
gtaagaaatattgaccatcttttgaatccccattttgactatgttgatttgtctcatgtttgattttccattatggctaaacctgtggtgctgtttccttattattccagGCTTCAGACTTCAGAGAAAACAAGATCCACACTGGTTGGCTGGATACAAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATCTCAGTGG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 13
---------------------gtaaattac--tcacatgacgagaaattattttatagaagctg-tttaaaatgctgaattgacat-tagtaaaatatt----tgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
||||| || | ||| | | | | || | || | || ||| || || | || | | || || || | || ||||||||||||| ||||||||||| ||||| || |||||||| |||| ||||| || ||||| ||| ||| |||||||| || |||||| |||| || |
gtaagaaatattaaccaccttttaaatcacattttcattatgttgattcatatcattaagtttgattttctattatggctaaacctgtggtgctattttcctattattccagGCTTCAGACTTTAGAGAAAACAAGATTCATACTGGTTGGCTCGACACCAGAATAGCTATGCGTGTTCAAGCTGAGAGGCCCCCATGGTATATTTCAGTGG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaattactcacatgacgagaaattattttatagaagctgtttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
||| || || || || ||| | | ||| | ||| | | || | | ||| | | | ||||||| || ||| | || |||||||||||||| |||||| |||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||| ||||| |
gtacgtttcttcttgcacacaaacttacactctg-----tgtatgcaataccctgacaagatcatttcaattgtcaacc--agGCTTCTGATTACCGTGATAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaattactcacatg--acgagaaattattttatagaagctgtttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
||| || | | | || || || || | |||| || | | | || | | | | | | ||||||| || ||| | ||||||||||| ||||| |||||| |||||||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||||| |
gtatgtttccttcttcctacatacaaaagttatactgtgactgt--aatgtaccctgacaagatcatttcgttgataaacc--agGCTTCTGATTACCGGGAAAACAAAATACACACTGGTTGGTTGGACAGTAGGATTGCTATGCGGGTCAGAGCAGAGAGACCTCCATGGTATCTCTCTGTAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 12
-------------------gtaaattactcacatgacgagaaattattttatagaagctg--tttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
|| | | ||| || || ||| | ||| ||| | | | | | || |||| ||| | |||||||| || |||||||| || ||||| ||||| |||||| |||||||||||||||| ||| ||||||||||||| ||||| || |||||||||||||| |
gtaaagttctaatctattgacaatcaaattccatttatcatcctttttcaataatttttaaccttagaatacaaactaaagaaaagaaaaaccttttctg-cagGCTTCTGATTACAGAGAGAATAAAATCCACACCGGTTGGTTGGACAGTAGAATTGCTATGAGGGTTAGAGCAGAAAGGCCGCCTTGGTATCTTTCTGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatagaagctgtttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
aattgacattagtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattactcacatgacgagaaattattttatagaagctgtttaaaatgctgaattgacattagtaaaatatttgatctcagGCTTCAGACTACAGAGAAAACAAAATTCACACAGGTTGGCTGGACAGTAGAATTGCAATGCGGGTTAGAGCAGAGAGGCCTCCCTGGTATCTTTCTGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG