Sequence
atgc intronic sequence ATGC exonic sequence...cctacataaatttcactcaataacaaataatgtttagaaaagaacatgtttctagcattcctcgtaatatcaaattcactcacaacttacgacattgcagGTGAATTGCATTGTGTTTGATAAGACAGGGACCCTCACAGTTGGGAAGCCAGTGGTTGTTACTACAAAACTCTTAAAAAAGACGTCACTTAGTAATTTCT
Basic information
species | Glycine max |
transcript | GLYMA01G42800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03640.t01 (Vitis vinifera), 3'ss of exon 2
cctacataaatttcactcaataacaaataatgtttagaa-aagaacatgtttctagcattcctcgtaatatcaaattca--ctcacaacttacgacatt--gcagGTGAATTGCATTGTGTTTGATAAGACAGGGACCCTCACAGTTGGGAAGCCAGTGGTTGTTACTACAAAACTCTTAAAAAAGACGTCACTTAGTAATTTCT
|| || | || | || || | || | | ||| || || ||| || || | | | | || || || | | | | ||| | |||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||||| |||| ||||| ||||| | | |||| | ||||
----cagaagtgccagttc-tatcagaatattcaaacagcaagcaccagtgtcttgcctttttaggacctttgaacacaatcttgaagttgattatattttgtagGTGAATTGCATTGTGTTTGACAAGACAGGGACCCTCACAGTTGGGAAGCCGGTAGTTGTTAACACAAGGCTCTTGAAAAATATGGCACTCCAAGAATTCT
upper sequence: GLYMA01G42800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 9
cctacataaatttcactcaataacaaataatgtttagaaaagaacatgtttctagcattcctcgtaatatcaaattcactcacaa--cttac--gacattgcagGTGAATTGCATTGTGTTTGATAAGACAGGGACCCTCACAGTTGGGAAGCCAGTGGTTGTTACTACAAAACTCTTAAAAAAGACGTCACTTAGTAATTTCT
| || | | || | | || || || || | | | | || | | | | ||| | || | ||| || |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||||| |||| |||| ||||| | | ||| | ||||
----tagaattattgttccaccagaatattcaaacagcaagcaaaactgtgttgccttttttaggacctttgaatataatcttgaggtttatttgattttgcagGTGAATTGCATTGTGTTTGACAAGACAGGGACCCTCACAGTTGGGAAGCCTGTAGTTGTTAACACAAGGCTCTGGAAAAATATGGTACTCCAAGAATTCT
upper sequence: GLYMA01G42800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 3
cctacataaatttcactcaataacaaataatgtttagaaaagaacatgtttctagcattcctcgtaatatcaaattca--ctcacaacttac--gacattgcagGTGAATTGCATTGTGTTTGATAAGACAGGGACCCTCACAGTTGGGAAGCCAGTGGTTGTTACTACAAAACTCTTAAAAAAGACGTCACTTAGTAATTTCT
| | || | | |||| | | || | | || || | | | || || | || ||||||| | || | || | || ||| ||||| ||||||| |||||||| |||||||| |||||||| |||||||||||||| ||||||| |||| ||||| ||||| | | |||| | ||||
-ttgtaataagtactgctgccaacagtt--tattcaaacaataagactggttttgccttgttggtg-tatcaaagataatcttggagctgatttgatcttgtagGTGGATTGCATCGTGTTTGACAAGACAGGTACCCTCACTGTTGGGAAGCCAGTAGTTGTTAGCACAAGGCTCTTGAAAAACATGGTACTTCAAGAATTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttctagcattcctcgtaatatcaaattcactcacaacttacgacattgcagGTGAATTGCATTGTGTTTGATAAGACAGGGACCCTCACAGTTGGGAAGCCAGTGGTTGTTACTACAAAACTCTTAAAAAAGACGTCACTTAGTAATTTCT
aacttac putative branch site (score: 2)
taatatcaaattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctacataaatttcactcaataacaaataatgtttagaaaagaacatgtttctagcattcctcgtaatatcaaattcactcacaacttacgacattgcagGTGAATTGCATTGTGTTTGATAAGACAGGGACCCTCACAGTTGGGAAGCCAGTGGTTGTTACTACAAAACTCTTAAAAAAGACGTCACTTAGTAATTTCT
cctacat
- - - - - - tcactca
- - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - catgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactcac