Sequence
atgc intronic sequence ATGC exonic sequence...tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
Basic information
species | Glycine max |
transcript | GLYMA16G27020.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G891739_T01 (Zea mays), 3'ss of exon 4
tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
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--------------gttcggtcatcttga----aggatgtatatataatcctattaatttt-gatcaactgataacctatttctgctgctt--tctgaagATTTCATTGAGTGGGCCTCATTCCATTCTGGGAAGGGCAGTTGTTGTACATGCTGATCCTGATGACCTAGGGAGGG
upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18100.2 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaa----tttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
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gtatatgatcttcttttttcacttcttcaatcatttaatgtttggcaaaataaacattacatttttcggttcttag-attgttcatatatctctcggacgtttcaccatttatctcatcttgtctttgaattcacagATACCGCTTAGTGGGCAGTATTCCATACTCGGGAGGGCGGTTGTTGTGCATGCGGATCCTGATGACCTTGGGAAAG
upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
tattgttttcatttggttgatatttttg--tttatga-aatttgaatgtagtttaattgggtctaga----acacttaatttcctc--tttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
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---------catttataaggtttctctagttttgtgataatgtgaaaactttttgattgattatagacttaaaagtttattccttcaactctttccttcaaatttgtagATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAGMapped 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|11274722|gb|BF325057.1|BF325057EST: GAGTTGCTGAGATTTCTATTAGAGATAGACAG ATTCCTCTAACTGGAGTTCACTCCATAATTGGAAAGGCCGTTTTTGTGCAT
genomic: GAGTTGCTGAGATTTCTATTAGAGATAGACAGgtaaagaatt ... caatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
ttctcac putative branch site (score: 2)
cttaatttcctctttc CT-rich tract
acttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattgttttcatttggttgatatttttgtttatgaaatttgaatgtagtttaattgggtctagaacacttaatttcctctttctcactttcaatatgtagATTCCTCTAACTGGAGTTCACTCCATAATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG