Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
Basic information
species | Glycine max |
transcript | GLYMA11G00980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02270.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
|||||||||||||||||||||||||||||||| || | |||| || |||
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTAN-TACTTGACCAGTTC-----------------------------------------------
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02020.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaattt--cccttcccttttgctcctacaaatgt-tctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
||| || |||| || || | | | | || | || | || | ||| | | |||| ||| | |||||||||||||||| |||||||||||||||||||| ||||| |||| || ||| ||||||| |||| ||||| ||||| ||| ||||||||||||||||
ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTCGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
-----gtaatttcccttcccttttgctcc----tacaaatgttctttcaaattgttttacaaa--ctagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
| | | | | | | ||| ||| || | | | ||| | ||| || | ||| | | |||| ||| | |||| |||||||||||||||||||||||||||||||| ||||| |||| || ||| ||||||| |||| || || ||||| || ||||||| ||||||||
ctattgaaccatttcgtggatgtaattcccaaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02010.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttc-ccttcccttttgctc--ctacaaatgttctttcaaattgttttacaaactagactagc-atacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
|||| ||| | || | | | ||| ||||| | | ||| | |||| ||| || || ||| |||||||||||||||||||||||||||||| |||||||| || || |||| || ||| ||||||| |||| ||||| ||||||||| | ||||||||||| |
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactaatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGAGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCACA
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttc-ccttcccttttgctc--ctacaaatgttctttcaaattgttttacaaactagactagc-atacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
|||| ||| | || | | | ||| ||||| | | ||| | ||| ||| || || ||| ||||||||||||||||||||||||||||||||||||||| || || |||| || ||| ||||||| |||| ||||| ||||||||| | ||||||||||||||
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaattt--cccttcccttttgctcctacaaatgt-tctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
||| || |||| || || | | | | || | || | || | ||| | | |||| ||| | ||||||||||||||||||||||||||||||||||||| ||||| |||| || ||| ||||||| |||| ||||| ||||| ||| ||||||||||||||||
ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02050.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttc-ccttcccttttgctc--ctacaaatgttctttcaaattgttttacaaactagactagc-atacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
|||| ||| | || | | | ||| ||||| | | ||| | ||| ||| || || ||| |||||||||||||||||||||||||||||| |||||||| || || |||| || ||| ||||||| |||| ||||| ||||||||| | ||||||||||| ||
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGAGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCACT
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
gtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagc-atacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT---------------
|||| ||| | | | | ||||| | | ||| | ||| ||| || || ||| |||||||||||||||||||||||||||||||||||||| || || |||| || ||| ||||| ||||||||| | |||||| |||| ||
gtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCA---------------GGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20558 (Selaginella moellendorffii), 3'ss of exon 4
gtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
|||| | | | || | |||| | | | | | |||| |||||||| |||||||||||||||||||| || || || || || |||||||||||| || || || || |||| || | |||||||| || |
-----------------------------gtgttaaactatgct-tctttctttctagtttcatgggctaacgaa-aaactgggtgtagGCTTTGATGGTGTTGAGATCCATGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAAATGGTGTCAACGATAGAACGGATGAGTATGGTGGTTCTTT
upper sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28624 (Selaginella moellendorffii), 3'ss of exon 4
gtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
|||| | | | || | |||| | || | | | | |||| |||||||| ||||||||||| |||||||| || || || || || ||||||||||||||| || || || |||| || | || ||||| || ||
-----------------------------gtgttaaactatgct-tctttctttctagtttcacaggctaacgaa-aaactgggtgtagGCTTTGATGGTGTTGAGATCCACGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAGATGGTGTCAACGATAGAACGGATGAGTACGGTGGTTCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
aaattgttttacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA