Sequence
atgc intronic sequence ATGC exonic sequence...tttttacattgtcagtgtataatccctttatctcatatatcacttgcacaaaaatgaatttgatattattttctatttcatttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
Basic information
species | Glycine max |
transcript | GLYMA09G15550.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G15550.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g13940.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------------------tttttacattgtcagtgtataatccct-ttatctcatatatcacttgcacaaaaatgaatttg---atattattttctatttcatttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
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gtaaactttctttatactgatgccaaaataattacaattttaagtcatattgtagttaggattcctcagttgtgtgcgggagcctgatgttcctttatgatatctttcctactgtgcattgggatgcctgcctactgtcagagttacctggaatttttttaactaaagagttatttttcctgttcagTTTGTCTCTCTGACTCAACCAATCAATGCGTTAGCTTTTGTTTTTGATGGTATCAATTATGGAGCATCAGATTTTGGATATGCTGCTTATTCAATG
upper sequence: GLYMA09G15550.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
tttttacattgtcagtgtataatccctttatctcatat-atcacttgcacaaaaatgaatttgatattattttctatttca-tttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
|| | | | | ||| ||| | || || || ||| | | ||| | | | | ||||| ||| | |||||| | || || || ||||||||||||| ||||||||||| || ||||| ||||||| ||| ||||| |||||||||||| ||||||||||| ||
-aaaaactgttttaaaaaacaattatcaaatcaaacattattttttatgtttgctcttttttaac-tcattcttaactcaaatttttggctttcgactacagTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG
upper sequence: GLYMA09G15550.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0064g00940.t01 (Vitis vinifera), 3'ss of exon 11
--tttttacattgtcagtgtataatccctttatctcatatatcacttgcacaaaaatgaatttgatattattttctatttcatttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
| | ||| | | | | | || | |||| | | ||| || || | | ||||| | ||| | | | ||||||||||||| || ||||| || ||||| || ||||||||||| || || ||||||| ||| ||||| |||||||||||||||||||||||| ||
gtatgtcccatatctaatatgcatttttttcttttcattttttgagctcac---gatcaactgaaa--tatttacccttttgtgatga-----------tagTTTGTTGCTGCAACTCAACCGATAAATTCTTTGGCCTTTGTCTTCGACGGCGTGAACTTTGGAGCATCGGATTTTGCATATTCTGCATACTCCATG
upper sequence: GLYMA09G15550.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
tttttacattgtcagtgtataatccctttatctcatatatcacttgcacaaaaatgaatttgatattattttctatttcatttt--taattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
| | ||| | ||| | | | | | || ||| | | || || |||| | | | || | | |||| | |||||||| ||| || ||||||||||| |||||||| |||||||||||||| | | ||||| || || || ||| | ||| |||| ||||| ||
-tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatccagcaataagta-aatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATGMapped 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|207688229|gb|GD670692.1|GD670692EST: TCTTCTCCAAAAGTGTTCTTGTTGTGCACTTAATCAGAATAGGCCTCCCG TTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGT
genomic: TCTTCTCCAAAAGTGTTCTTGTTGTGCACTTAATCAGAATAGGCCTCCCGgtataatcat ... tactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGT
EST:
gi|298168058|gb|HO013321.1|HO013321EST: TCTTCTCCAAAAGTGTTCTTGTTGTGCACTTAATCAGAATAAGCCTCCCG TTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGT
genomic: TCTTCTCCAAAAGTGTTCTTGTTGTGCACTTAATCAGAATAGGCCTCCCGgtataatcat ... tactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacaaaaatgaatttgatattattttctatttcatttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
ttttaat putative branch site (score: 3)
ttttactc CT-rich tract
aaaatgaatttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttacattgtcagtgtataatccctttatctcatatatcacttgcacaaaaatgaatttgatattattttctatttcatttttaattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
- - - - - - - - - - - -cccttta
- - - - - - - - - - - - - - - - - - - - - cttgcac
- - - - - - - - - - - - - - - - - - - - - - - - - aaaatgaa