Sequence
atgc intronic sequence ATGC exonic sequence...cagtattacctctagcttcaatacctatgttttgaattgagcaatgttattgcaattgtttaatctgctaacattgtttagtattgctttcccgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
Basic information
species | Glycine max |
transcript | GLYMA13G44940.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G44940.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G73110.1 (Arabidopsis thaliana), 3'ss of exon 6
--cagtattacctctagcttcaatacctatgttttgaattgagcaatgttattgcaattgtttaatctgctaacattgtttagtattgctttcc-cgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
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gttagaagcgtttct--ttaccattcccattccccagtcttacttaacctatt-tatctatatgggtttggaatgaactttgatgatgattttgataatgcagGGAAAGATGAGTGTTCTCATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
upper sequence: GLYMA13G44940.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0018g01270.t01 (Vitis vinifera), 3'ss of exon 6
cagtattacctctagcttcaatacctatgttttgaattgagcaatgttattgcaattgtttaatctgctaacattgtt-----tagtattgctttcccgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
| || ||| || ||| | |||| | ||| || | |||| | |||||| | ||| ||| | | || ||| | ||||| || ||||||||||| ||||||||||| |||||||||||| |||| |||||||
--tgaatatttctgattt--atatcaatgtcct-aatggatgtttcttatcgactttgtttgagtacttaatgcagttatggttgattttccttgactaccgcagGGGAAGATGAGCTGTTTAATGATCAATGACATTGATGCTGGCATTGGGAGATTTG
upper sequence: GLYMA13G44940.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ31275 (Selaginella moellendorffii), 3'ss of exon 5
cagtattacctctagcttcaatacctatgttttgaattgagcaatgttattgcaattgtttaatctgctaa--cattgtttagtattgctttcccgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
|| ||| ||| | | || || | |||| | || | || |||||||| ||||||| |||||||||| ||||||||||||||| |||| ||||||
---------------------------------------------gtacgtgctgcgacttactggacaaaagcactctttaacgtctctgtacc-----agGGAAAACTGAGCTGCCTGATGATCAACGATATTGATGCTGGCATTGGGCGATTTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|5175439|gb|AI759772.1|AI759772EST: AATTGATTCGTGAACGCTATAGAACAGCATCTCAAGTGGTCCAGAATCAA GGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGA
genomic: AATTGATTCGTGAACGCTATAGAACAGCATCTCAAGTGGTCCAGAATCAAgttaggagtt ... cccgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttattgcaattgtttaatctgctaacattgtttagtattgctttcccgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
tgctaac putative branch site (score: 1)
ttgctttccc putative PPT
aattgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagtattacctctagcttcaatacctatgttttgaattgagcaatgttattgcaattgtttaatctgctaacattgtttagtattgctttcccgatacagGGAAAAATGAGCTGTTTGATGATCAATGATATTGATGCTGGCCTTGGTAGATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - -agcttca
- - - - - - - - - - - -cctatgt
- - - - - - - - - - - - - - - - - - - -agcaatg
- - - - - - - - - - - - - - - - - - - - - - - -tattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctaac