Sequence
atgc intronic sequence ATGC exonic sequencegtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcaggttgttttcatactaattttgaagttatgaaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
Basic information
species | Glycine max |
transcript | GLYMA08G10180.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 14
gtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcaggttgttttcatactaattttgaagttatgaaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
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---------------------------------------------gtaatattcgtcatctaatttgtgtggggtggggtgggtacgtcgagtttgggtgtgtcatcaggct-taactaaggtaatgctg----tgtgtt-tccagGTGAATGCTATTCAGATGAAGGAGACGGTTGAAGAAAACACAAGCACAACTGAGAGAGTATTCCAGGACAGACAGTATCAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 14
lower sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 2
gtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcaggt-tgttttcatactaattttgaagttatgaaatgc-agGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
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------------------------------------------------------------------------------gtaatatatgtacacatacactttggatctgatatggtcatcaatctttactgttgttatgcacttccagGTAAATGCAATTCAAATGAAGGAGACGGTAGAAGAAAACACGAGCACCACTGAGAGAGTGTTCCAGGATCGGCAGTATCAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 14
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 14
gtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcag--gttgttttcatactaattttgaagttatgaaatgc-agGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
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------------------------------------------------------------------------------gtaatgtatgtacacatacactttggatttgacatggtcattaagcttgaactgttgttttgcgcttccagGTAAATGCAATTCAAATGAAAGAGACGGTAGAAGAAAACACGAGCACCACTGAGAGAGTGTTCCAGGATCGGCAGTATCAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 14
gtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcaggttgttttcatactaattttgaagttatg---aaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
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--------------------------------gtacgttggtt--tttttcttggtctcttcacttaaagt--atcctagaatcttgtgata--ctgttttgtatgtagcttatagtgaagcaattctttcttttgttcctgggtgcagGTAAATGCGATCCAGATGAAAGAGACAGTAGAGGAGAACACAAGTACAACGGAAAGAGTATTCCAGGACCGACAATACCAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 14
gtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacct-caaaattaaaaactcagtataaatttttctttaa-tcaggttgttttcatactaattttgaagttatgaaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
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-------------------------------------------gccactcaa--atatttacagtcagcttatgacattgttatgtcttttctaattgttactcaacttatggaggttgaagtttgcatttt---tttttaaatacagGTAAATGCAATCCAAATGAAGGAAACAGTGGAGGAGAACACAAGCACCACTGAAAGAGTGTTCCAGGATCGTCAATATCAGMapped 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|21285971|gb|BQ473842.1|BQ473842EST: ACTTATTTGTTTTTAATGATGGGTTTACAGCTCCTCTTTACCGTATAAAG GTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACC
genomic: ACTCATTTGTTTTTAATGATGGGTTTACAGCTCCTCTTTACCGTATAAAGgtattactca ... tgaaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttttctttaatcaggttgttttcatactaattttgaagttatgaaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
tactaat putative branch site (score: 1)
ttttcatactaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattactcattgcttttgaacacttggtctcatatattggatgaatctgaactgtgttttaattcaacctcaaaattaaaaactcagtataaatttttctttaatcaggttgttttcatactaattttgaagttatgaaatgcagGTGAATGCAATTCAATTGAAGGAGACAGTCGAGGAGAACACAAGCACCACCGAAAGAGTTTTCCAAGACCGTCAGTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA