Sequence
atgc intronic sequence ATGC exonic sequence...ccccattagctatgctatatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
Basic information
species | Glycine max |
transcript | GLYMA18G45120.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g60190.2 (Oryza sativa), 3'ss of exon 2
ccccattagctatgctatatagtctatatttcttagttttaaaattattcatagcatg--tgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
|| ||| | | | | || || ||| || ||| | | || | || || | | || | | ||| ||| | ||||||||||||||| ||||||||||| |||||||| ||||||| ||| ||||| || ||||| ||||| || ||||||||||| || || || |||| ||
---------gtaagctgt-tgttgagttttgattcatttgggaactataggttggatcactctgcatgttttgtgacaagcgtgtttcatt-ctcactgtagTGCTAAGCTTGTGGACCTTGCTCTTGCCTCTGGGAAAATTTATGATGGAGAGGGGTTCAATTACATCAAAGAATGTTTTGACAAGGGTACCCTGCACCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 3
-ccccattagctatgctatatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatat-cttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
|||||| | ||||| | | | ||| || ||| || | | | |||| | ||| ||| | || ||| ||||| ||||| || |||| | ||||||||||||||||||||||||||||| || |||||||| ||||| ||||||| | ||||| | |||||
ttgccatta--tgccgtatatgaaatcattcttttaagaaagaagttagaagcctcagacttaagcctctaaatataccatgttctccattttcttttgtagGGCTAAACTTGTGGATACTGCTTTGGCCTCTGGAAAAATTTTTGAAGGAGAAGGGTTTAAGTACATTAAGGAGAGTTTTGACCAAGGCACTCTTCATCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 3
ccccattagctatgcta--tatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
|| | ||| || ||| | | | | |||| | || | |||| |||| | | | | | || || | ||||||||||||||| || | ||||| ||||| ||||| |||| ||| ||||| || ||||| ||||| || |||| |||||||||||| || | || ||
-tttgtttgtcatgttagtcttagataaaacctttagtccttaagagtacatactagatgttctctgatctgactgagt-actgcattctttttgtctatagTGCTAAGCTTGTTGATCAAGCTCTTGCCTCAGGAAAGATTTATGATGGAGATGGGTTCAACTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 3
---ccccattagctatgcta--tatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
| | ||| || || ||| | | | |||| | | | |||| |||| | | | | | | | | |||||||||||||||||| | ||||| ||||| ||||| |||| ||| ||||| || ||||| ||||| || |||| |||||||| ||| || | || ||
ctattttgtctgtcatgttagtcttaaataatacctttagttcttaagagttcatactagatgttctctgatctgagtgctgcattcttt-----ctaactatagTGCTAAGCTTGTCGATCAAGCTCTTGCCTCCGGAAAGATTTATGATGGAGATGGGTTCAACTACATCAAAGAATCTTTTGAAAGTGGTACTCTTCACCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053420_T01 (Zea mays), 3'ss of exon 4
ccccattagctatgcta-tatagtctatatttcttagtt-ttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
| ||| | ||| || | | || | ||||| |||| | | | |||| |||| | | | | | || || | ||||||||||||||| || | ||||| ||||| ||||| |||| ||| ||||| || ||||| ||||| || |||| |||||||||||| || | || ||
-cacatctgtcatgttagtcttaaataaaacctttagtccttaagagttcatactagatgttctctgatctgactgagt-actgcattctttttgtctatagTGCTAAGCTTGTTGATCAAGCTCTTGCCTCAGGAAAGATTTATGATGGAGATGGGTTCAATTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146778_T02 (Zea mays), 3'ss of exon 6
ccccattagctatgctatatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
|||| | ||| | || || | |||| | | || | ||| |||| |||| | | | | | || || | ||||||||||||||| || | ||||| ||||| ||||| |||| ||| ||||| || ||||| ||||| || |||| |||||||||||| || | || ||
----gttagtcttaa-ataaaacctttagtcctta-----agagttcatactag-atgttctctgatctgactgagt-actgcattctttttgtctatagTGCTAAGCTTGTTGATCAAGCTCTTGCCTCAGGAAAGATTTATGATGGAGATGGGTTCAATTACATCAAAGAATCTTTTGAAAATGGTACTCTTCACCTT
upper sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 2
ccccattagctatgctatatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttc----attttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
| || | |||| || | ||| |||||| | ||| | | |||| | ||| | || || | | || || | | |||||| |||||||| || ||||||| | |||||| || || | ||| |||||||| || ||||| || ||||| |||||||||| |||||||||||| |||
tttcttttga-atgcaat-tgttctt--tttcttgccaattgtattttctgtggcatatcaagtgagttatccattgtgaagtttatttattttctgaatgtagTGCAAAGCTTGTTGATTTTGCTCTGGACTCTGGGAAGATCTATGAGGGAGAAGGCTTTAAGTATATCAAGGAGTGTTTTGAAACTGGCACATTGCACCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
ttcatttt CT-rich tract
ttcatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccccattagctatgctatatagtctatatttcttagttttaaaattattcatagcatgtgtgatgattgggatatcttggtttgtgattgttcattttagTGCTAAGCTTGTCGACCTTGCTCTAGCCTCTGGAAAAATTTTTGAAGGAGAAGGTTTCAAGTACATAAAGGAATGTTTTGAAAATGGCACATTGCATCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
ccccatt
- - - - -ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgtg