Sequence
atgc intronic sequence ATGC exonic sequence...ggagtgggaggggtgggattatgtttatattttcatgatcttatcaatgaaatctatattctgcgtacctgtaatgttgtttatccatgggcacctgcagATGACCACAAACCATTCATTGGACACATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC
Basic information
species | Glycine max |
transcript | GLYMA06G16680.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 8
--ggagtgggaggggtgggat-tatgtttatattttcatgatc-ttatcaatgaa-atctatattctgcgtacctgtaatgttgtttatcc-atgggcacctg-cagATGACCACAAACCATTCATTGGACACATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC---
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gtataattttattgtcacgttcttcgcaaaaggcttcataattattagcattacataattatatttgttgtgacaatgatatagaagctcttgctactatctgactgcagACAGTGAAGCGCCACAAGAACCAGCTAAACACCACAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCAAATATCATCAATCAGATTGATACTCT
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
ggagtgggaggggtgggattatgtttatattttcatgatcttatcaatgaaatctatattctgcgtacctgtaatgttgtttatccatgggcacctgcagATGACCACAAACCATTCATTGGACACATGAG-----CAATCGCCA---AAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC---
|| || ||| | ||| ||||| | | | | | ||| | ||| | | ||| |||| || | | | | | || || || | | | | |||| || ||| | ||| |||||||| || ||||||||||| ||||||||||| ||||| | ||| ||||| |
---------ggttcttgaccctgtacaatagttcttgatcctgtgatttagttcttgaccctgtg-atatgtggcattgtctaaagtttctttcttttatcttactgcagAC-AGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G08660.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------------ggagtgggaggggtgggattatgtttatattttcatgatcttat-caatgaaatctatattctgcgtacctgtaatgttgtttatc----catgggcacctgc--agATGACCACAAACCATTCATTGGACACATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC
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gtatgtaagttcctcctttttgtaccttcaccatgtgctactgagcatgtatctaagcttttgattttttctctcgtccactactcttttttactacatgctctaatatatcttgttaattgatcctccataattaagttttcacgcaaca-acctgaattttcttatattaaattatttttctttgcccagATGATCAACCATCGAAGAAAGGAGCTGCAGAATATGATAAAAGATTGGGACCTGCTGGTCTTGCTTTACATTATGCAAATATAATTGTGCAGATTGACAC
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g02970.t01 (Vitis vinifera), 3'ss of exon 7
-------ggagtgggaggggtgggattatgtttatattttcat--gatcttatcaatgaaatctatattctgcgtacctgtaatgttgtttatccatgggca-cctgcagATGACCACAAACCATTCATTGGACACATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC
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ttgtccttacctaaaaggatctaggtaatgtcaatagagccagtggttcttataaaagaaata--------aggcatctg--ataatgtttccttatgggcaacctgcagATAGTGATACACCTGTAAATGGATCTGTGAGTGATCATCAAAGATTGGGACCTGCTGGTCTTGCATTGCATTATGCAAATATTGTTATGCAAATTGATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgaaatctatattctgcgtacctgtaatgttgtttatccatgggcacctgcagATGACCACAAACCATTCATTGGACACATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC
aatctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggagtgggaggggtgggattatgtttatattttcatgatcttatcaatgaaatctatattctgcgtacctgtaatgttgtttatccatgggcacctgcagATGACCACAAACCATTCATTGGACACATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-gagtggg
- - - - - gggtggg
- - - - - - - - - - - - - - - - -catgatc
- - - - - - - - - - - - - - - - - - - - - - caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgtac