Sequence
atgc intronic sequence ATGC exonic sequencegttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
Basic information
species | Glycine max |
transcript | GLYMA08G20100.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
| ||| | | | | ||| | | | ||| |||||||| | | ||||| ||| || || || || ||||| | |||||||||||||| |||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||||||||||| | |||||||||| |||||||| |
---------------------------------gtgattg--actatctatattcaaataatgtaca--aattctgttatgc-----gcttcatacatcctcttgctgaca-tttttattcaa-----------tatcagGAAAGAGATGTCAGTGAAGAATCTGGATGGAAGCTTGTCCATGGGGATGTTTTCCGGCCTCCTCGCAGTTTGGCTCTTCTTTCAGCCCTTGTTGGTGTTG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| ||| |||||| | || ||| || | | ||| | ||| | || || | | ||| |||| || | | || | | |||||||||||||||||||| |||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||| ||||||| ||| ||||||||| |
------------------------gtgactggacgaattatt----tgaatattcata-gcaaatcattttgcattattttcatctaatctcttgatagtt----ttgttaacttatatttttctttta-------tcagGAAAGAGATGTTAGTGAGGAATCTGGTTGGAAGCTTGTCCATGGAGATGTTTTCCGGCCTCCTCGTAGCTTGGTGTTTCTTTCTGCTTTTGTTGGTATTG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| | ||| || || || | ||| | || | | | | || | |||| ||||||| | | || | | || || |||| ||||| | | || | || |||| |||||||||| ||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||||||| ||||||| || |||||||| | |
----------------gtatatctac--cttttgtt-taattgtattcttagctctagcatctaagttggatt-tgttttcacctagtgc-cact-cgattgggacc-tcaagtcttgat--attcc----ttttgttagGAGAGAGATGTTAATGAGGAATCTGGATGGAAGCTTGTTCATGGTGATGTATTTCGCCCTCCTCGAAGTTTGGCCTTTCTTTCTGCAGTTGTTGGCATCG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 6
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| || | | | || | || | |||| | || |||| || ||||||| || ||||| ||| | |||| || | || ||| || || | | | ||||| ||||||| | |||||||||||| ||||| ||||| |||||||||||||| ||||||||| ||| | | ||| ||||||||||| ||||||||| |
gtgagtttctatatatatgatcatggtgttatt-ccagtagcgtttt-aatatttatgc---------aggttctgattt--taattagtttatacttgtatcctttgctgatatacatt--------agtttgtattagGAACGAGATGTCAATGAAGAATCTGGATGGAAGCTTGTACATGGTGATGTTTTCCGGCCTCCTTGCAATCTAGTTCTTCTTTCAGCTCTTGTTGGTATTG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
| || ||| | || | | || |||| | ||||| || | | ||| || || ||| | || | ||| ||||| ||||||||| ||||||||| || ||||| ||||| ||||||||||| || ||||||||||| | ||| ||||||| || | ||||||| |
------------------------------aataaaattgaatcatacaagttccaagta-acaacaagtaacaagtttttctttga----ctcgatggatc--gtttaggattaagatacagttttc---ctttttcagGAGCGAGATGTTAATGAAGAATCCGGGTGGAAGCTTGTCCATGGTGATGTGTTCCGGCCTCCTCGTGGCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaa----atatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| | | | | | || | || || | |||| || | |||| ||| | | | || || | | | || ||| ||| | || | | |||| |||| |||||||||| ||| ||||| || ||||| ||||| |||||||| || ||||||||||| || |||||| | ||||||| || ||||||||| |
----------------gtgaggagctgaattctggcgcgcctactgtttaactgtatgcttgatagctagagaaatgttttcactagattttgctg-gctccccccactccattgttgcttaagttatgatattacctttctagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGTGACGTATTTCGGCCTCCCCGAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
| | | || || ||| | | |||||| || | | | | | |||||| | | || | | | ||| | | || ||| |||| |||||||||| ||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| | |||||| | ||||||| || ||||||||| |
---------------------------aaacatgccttaatagttagagaaacattttcac------tagattttgctggcttctgcactccattgttgcttaagttatgatatattgat--attacc-----tttttagGAGAGAGATGTTAATGAGGAATCAGGATGGAAGCTTGTCCATGGCGATGTATTTCGGCCTCCCCAAAGTTTGATGTTTCTTTCTGCACTTGTTGGTATCG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattattttt---------aaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtg-gttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| | | || || | ||| | ||| | || | | ||| ||||| || | | | | | | | || || | | | || | | || | || |||| | | | |||||| | ||||| |||||||||||||| ||||||||||||||||| ||||| || |||| | | ||| | ||| | || ||||| || ||||||||||
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattga-tgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
||| | || | | || |||| || || | |||| | ||||| | ||| ||| || | ||||| | | || ||| || || |||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||||| |||||||||| || ||| ||| | ||||||||||||||||| ||||
-----------gtgacactc-tcaacttttgtttatattctttttcctttaattggtttgtgggat-----ttccatttc-------------------ttttaattgtaa---ccattttaacatgtaa---ttctcagGAAAGAGATGTGAGTGAAGAGTCTGGCTGGAAGCTTGTTCATGGGGATGTTTTCCGGCCTCCTCCCAATTTAGTTCTACTTTCAGCTGTTGTTGGCACAG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| | |||| | | || | | | | | | || | || | |||| | | | | || ||| | || | || || | | ||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||||||||| ||||||||| | ||||| | |||||||||||||||| || |
----------------------------gtaatgctattttaagttcttgactgtgtctatg---tttttttttttttttaatatatatagtccttaagtgaaaattatgtatcttatttt--ccactatatattgtcagGAAAGGGATGTAAGTGAAGAGTCTGGCTGGAAACTTGTCCATGGGGATGTTTTTCGGTCTCCTCGCAATATGGTTTTATTTTCAGCTGTTGTTGGCACTG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| | || ||| | | || | | | || || |||||||||||| || || |||||||| ||||| ||||| ||||| || |||||||| || | || || ||| | | ||| | || || | |||||||||| |
----------------------------------------------------------------------------------------gtacgtttatgttgcgcattgcagt---ggctgaa----agaacttttccagGAAAGGGACGTGAGTGAAGAGTCTGGATGGAAGCTTGTCCACGGTGATGTCTTCAGACCGCCACGCTATCTTGTTTTGCTGTCTTCGCTTGTTGGTACCG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 7
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
|| | || ||| | | || | ||| || || |||||||||||| || || |||||||| ||||| ||||| ||||| || |||||||| || | || || ||| | | ||| | || || | |||||||||| |
----------------------------------------------------------------------------------------gtacgtttatgttgcgcattgcagtgtttg--aaa-----gaacttttccagGAAAGGGACGTGAGTGAAGAGTCTGGATGGAAGCTTGTCCACGGTGATGTCTTCAGACCGCCACGCTATCTTGTTTTGCTGTCTTCGCTTGTTGGTACTGMapped 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|207797994|gb|GD768096.1|GD768096EST: GAAATGACTATGCAAAGTATGCTCGGGAAGATGGTGATTTGGAAACTCTG GAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTT
genomic: GAAATGACTATGCAAAGTATGCCCGGGAAGATGATGATTTGGAAACTCTGgttaggcttt ... atatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
ttctgat putative branch site (score: 3)
tatttcc putative PPT
aaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggctttcttgatgtttgtctgttactattattattattatttttaaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtggttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT