Sequence
atgc intronic sequence ATGC exonic sequence...attgtatatatatttctggtttggtgacttttcagttattatttgatacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
Basic information
species | Glycine max |
transcript | GLYMA16G26140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------attgtatatatatttctggtttg-gtgacttttcagttattatttgatacatgtcactcttgaatgttatgtatctgaatgtgt-gcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
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gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgct-tttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttg--gtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 3
attgtatatatatttctggtttggtgacttttcagtt-attatttgatacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
|| ||||| | || | ||| | || ||| || | | ||| ||| || | || |||| | | | | | | |||| | || ||||| ||||||||||||||||||||||| || || || || ||| ||||||| ||||| |||||||| ||||| || | | || | |||
-------gtaagtttctcggtttttcgttttcctgtccgttagtttctg-acatcagtct---atataattcatctcattctccttgggaattt---gcagAGAAACTATCGATTCTTCTTCATGTTTGTCTTCTCCACGACTCTTCTCTGTGTATATGTGTTCGCCTTTTGTTGTGTCTACATAAAGAAGATCAAAGAGT
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 3
attgtatatatatttctggtttggtg-acttttcagttatt-atttgatacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
||| | | || | ||| || ||| | | | ||| || | ||| | || | || | | ||||| |||| | || || || |||||||||||||| |||||||| || || || || ||||||||||| || || || || ||||||||||| |||| ||||||||
---gtaagtcaaaatccaactgatcccgtctttaagctatccacataaaccatagt-ttcctaaatatcatctc-----atattctgatggttgtt--gcagAGGAACTACCGATTCTTCTTCATGTTCGTCTTCTCCACGACCCTTCTATGTATATATGTGTTTGCCTTCTGCTGGGTCTATATAAGAAAGATTATGGAAT
upper sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
attgtatatatatttctggtttggtgacttttcagttattatttg-atacatgtcactcttgaatgt-tatgtatctgaatgtgtgcacaattgtta-tgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
| | | | || || || | || || || | | || | | | | ||| ||||||| | ||||||| | |||||||||||||||| || |||||||||||||||||||| || || || |||||||||||||| || | || || ||||||||||||| || || |||||
---ttttccagttgtcatcttcaccaacatgataggaatgatgcatgtgcttgaatttgtgggcaatgcatgaatctgaacactttcacaattctgggtgcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTTGGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
atttgat putative branch site (score: 5)
aattgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtatatatatttctggtttggtgacttttcagttattatttgatacatgtcactcttgaatgttatgtatctgaatgtgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG