Sequence
atgc intronic sequence ATGC exonic sequence...aaaggaaagtaaagtattgtgtgatttacacattttaaatccctattaatttctagtccattgattatttatttcttcttttttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
Basic information
species | Glycine max |
transcript | GLYMA16G00400.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 5
-aaagg--aaagtaaagtattgtgtgatttac--acattttaaatccctattaatttctagtccattgattatttatttcttcttttttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
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caatcgttggagtcaaacaatttctagctgccttaccttttagtgtcatacccaatcgcagatttctgctt-----tgcattaatttatctaatttgtcctgcagATATGCCGAGCGCTTGCTTATATACATAACTGCATTGGCATCTGCCACCGTGATATCAAACCGCAGAATGTTCTT
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 5
--------------------aaaggaaagtaaagtattgtgtgatttacac--------attt-taaatccctatta-atttctagtccattgattatttattt--cttcttt------tttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
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gtaactatttcctacatttgaaccttttttaatcttttttgtagtttttgcttcataatatttgtaaatgcatgccagattgataatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG
upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 4
--aaaggaaagtaaagtattgtgtgatttacacattttaaatccctattaatttctagtccattgattatttatttcttctt-ttttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
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aaaaacatatgtagcttattttatcact-gtaagggttatgtactgg--agttgataattgatttatcatgcattactaattattctcttactctggttgtagATCTGCAGAGCGCTTGCGTATATACATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTTMapped 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|26047783|gb|CA784461.1|CA784461EST: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAG ATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
genomic: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAGgtatgtaatt ... ttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
EST:
gi|26048721|gb|CA785174.1|CA785174EST: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAG ATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGGCATCGT
genomic: GGATTAACCAGCGAATGCCTTTAATATATGTAAAGCTTTATACCTACCAGgtatgtaatt ... ttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatttctagtccattgattatttatttcttcttttttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
ttatttatttcttctt CT-rich tract
attatttatttcttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaggaaagtaaagtattgtgtgatttacacattttaaatccctattaatttctagtccattgattatttatttcttcttttttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT
aaaggaaa
- - - - - - - - -tgtgtga