Sequence
atgc intronic sequence ATGC exonic sequence...gccagatgctgctaacttgtccctcataggaattgttcttggtattagaactatcaacagatatcaagattttatcaccttctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
Basic information
species | Glycine max |
transcript | GLYMA04G12500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G109039_T01 (Zea mays), 3'ss of exon 6
gccagatgctgctaacttgtccctcatagga-attgttcttggtattagaactatcaacagatatcaagattttatcaccttctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
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cccagcagttccctggcaacaacttatatctcagttctctgtgtgctctccatattgatcttttgttcaattgaatatcttctgttgatgtca-aatgcagCACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G048045_T01 (Zea mays), 3'ss of exon 6
-gccagatgctgctaacttgtccctcataggaattgttcttggtattagaactatcaacagatatcaagattttatcaccttctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
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agctgatggatgtgcatgtgtttacatggttaatctttctgtgtgttctccatactgatcttttgttcaattg-attatcttctgttgatgtcatatgcagCACCTTGATCGGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAG
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55680.1 (Arabidopsis thaliana), 3'ss of exon 6
gccagatgctgctaacttgtccctcataggaatt--gttcttggtattagaactatcaacagat--atcaag--attttatcaccttctttgttactggaatg--cagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
| || | | | || | |||| | || ||| || | | || || || |||||| | || ||| ||| || | || ||||| || ||| |||||||||| |||||||| | | || |||||||||||||||||||| |||||||| |||||||||||| | || ||
gtaagctctag--agttttacaatcatggatttttagtttttcacacaacaattacatgcattctaatcaaggaacttcatctttttccacattgattttattttcagCATCTTGATAGACCTGGTGTGAGCTTTTGTTCACGTACTACTTATGATGATAATGCTATAACCAATGCTATTGAGATTTATAACAAACCCAG
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13340.1 (Arabidopsis thaliana), 3'ss of exon 6
gccagatgctgctaacttgtccctcataggaattgttcttggtattagaactatcaacagatatcaagattttatcaccttctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
| || | || || ||| | ||| || ||| || | | | | || || || || || ||| | ||||| || ||| |||| ||||| ||||||||| | | | |||||||||||||||||||| |||||||| |||||||| || | || ||
----gtaactctagatttatctatcac--ggattaatcacattatc-gacttgcaattctgttctatgagatt--catctgtttc--cactttggttcagCATCTTGATAGACCGGGTGTCAGCTTTTGCTCTCGTATGACTTATGATGATAATGCTATAACCAATGCTATTGAGATCTACAACAAACCCAG
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0015g01750.t01 (Vitis vinifera), 3'ss of exon 5
gccagatgctgctaacttgtc---cctcataggaattgttcttggtattagaactatcaacagatatcaagattttatcacct-tctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
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gttac-ttctgtcatttttcataaccttgtagttattaaatcaggtcctgaaa--attaatt-acactgagactgaggcattcaccccttttattggaatgcagTATCTAGATCGACCTGGAGTTAGTTTCTGTTCCAGGATAACTTATGACGATAATGCAATCACCAATGCTATTGAGATTTATGCCAGTTCCAGMapped 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|192298146|gb|FG991666.1|FG991666EST: AGGAGAAGCTTCTAGTTGTTGGAGGATTTCAGGGTGAACTTATTTTTAAG CACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGAT
genomic: AGGAGAAGCTTCTAGTTGTTGGAGGATTTCAGGGTGAACTTATTTTTAAGgtaatttgac ... tggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaactatcaacagatatcaagattttatcaccttctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
ccttctttgttact CT-rich tract
atatcaagattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccagatgctgctaacttgtccctcataggaattgttcttggtattagaactatcaacagatatcaagattttatcaccttctttgttactggaatgcagCACCTAGATCGACCTGGTGTTAGCTTTTGCACGAGAACAACTTATGATGATAATGCTATCACCAATGCCATTGAGATTTATGATTGTCCTAG
- - -atgctgc
- - - - - - - - - -tccctca
- - - - - - - - - - - - - - - - - gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - atcaaca