Sequence
atgc intronic sequence ATGC exonic sequence...tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
Basic information
species | Glycine max |
transcript | GLYMA15G02640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
-tacgtga-ttttgtgcacat-tgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| |||| || | || || | | | || | || | | | | | | | | ||| ||| | | || ||| | | | || || || || || | ||||||||| |||||| |||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||
ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatcatgagcatgaagctaatacc-atgttctcatattgtt--ttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttc--tagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| | |||||| | | | ||| ||| | | || || | | | || || || | | | ||||| || |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||| ||||||||||| ||| ||||||| || ||| ||
--tttgctgatgtgcatctcatatacattcgattagatgtaatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
----tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| |||||| | ||| || || || | ||| | |||| | || | ||| | || ||| | ||| || || |||||||| || || |||||||||||||||||||| |||||||||||||| ||||||| |||||||||||||| |||||| ||||||| |||||| ||
tatgttgctgatttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaac----ctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatg-gtgttat--gttgctcatattttc-tagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
|| | | ||||| | | | | || | | | ||| |||| || | || | ||| | |||| || ||||| || |||||||| || || |||||||||||||||||||| |||||||| ||||| ||||||| |||||||||||||| |||||| ||||||| |||||| ||
---ttgctgatttgcacctcttatatcttaaatgtatgctgccatt-ttttgtattgtcctattgggtagtgatatatattatttgtaatctttatttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttct-------agCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
||| | || | | | | ||||||| | | | ||| ||| || | | | | | || | |||| |||| || | | |||||||| ||||| ||||||||||| |||||| |||||||||| |||||||| | |||||||||||||| || ||||| ||||||||||| || ||||||
----tgaatgagttaatgtggctgagttttttttgga--tcttatattttgctgcctgggtttattactatggtgataccatgtc-ctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
tacgtgattttg-----tgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcat-attttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | | || |||| ||| || || || || | ||| || | | | || || || | || | || | | | | || |||||||| || ||||||||||| |||||| | ||||||||| | |||||| ||||||| | || || || ||||| ||||||||||| |||||| ||
ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacat----ttgtgggcattgtattgatacatat--tcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctc----atattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | ||||| | | | || || | | || ||||| | || | || | | |||| | | | || | | || || || || ||||| || || || ||||||||| ||||| ||||||| ||||| ||||||||||||| || ||||| |||||||||||||| ||||| ||
ttattctctttgtcgaaaatcttgttgatcct----aaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
------tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| | | | ||| | || || || | || ||| ||| | |||| || || | || | || | || ||| || ||||| || ||||| || || || ||||||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttt---tctcttataatt---agCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
--tacgtgattttgtgcacattgtttttatt--tttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
| ||| || ||| || | | | || | | || || || || || | | |||||| | || | |||| ||| | || || ||||||||||| || ||||||||||||||| |||||||||| ||||||||| ||||||||||||| ||||| || |||||||||||||| |||||||||
gaaagactattatggaaacaatgctaatggtaacttgtttatttctcttatttgggtacgatttagtgaaattttgctgat----tgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA
upper sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 6
tacgtgattttgtgcacattgtttttattttt-ttaaaattttcatagttttctagatactga--tcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
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---tcgtttttttcttcttcattttcactagtacctatatttatattggtggatagttattcagtcttactttgaattacattttttatcttgttgtttgcagTGACTGTGAAACGTACATATCTGCTGATGATCTGAGAATTAATTTATGGAACATGGAGATCAGTGACCAAAGTTTCAATATTGTTGATATTAAGCCTGTCMapped 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|11274020|gb|BF324388.1|BF324388EST: GTGTATGCACACGCTCATGATTATCACATCAATTCTATTTCAAATAACAG CGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAA
genomic: GTGTATGCACACGCTCATGATTATCACATCAATTCTATTTCAAATAACAGgtattttagt ... tattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
tactgat putative branch site (score: 2)
tattttct putative PPT
atattttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA
- - - - - - tgcacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct