Sequence
atgc intronic sequence ATGC exonic sequencegtaatctcttgcattagttcttgtcaattgaccctaaaaactcatgcttctgtttgactagttttggctctcaagcatctgaatctttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
Basic information
species | Glycine max |
transcript | GLYMA06G16700.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 16
-gtaatctcttgcatta-gttcttgtcaattgaccctaaaaactcatgcttctgtttgactagttttggctctcaagcatctgaatctttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
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cttcagctgatgtatttcgttgatgctaatgtacctgtagaatgtaccaaggaattaaagaaaattttcctattgcttag-tggatatttt--------gtttgtgcagATGGTTGGCGATTTCTTTGATCAACTGAAATCACGAAGTAAAGGATATGCTAGCATGGAATATTCAGTTGTTGG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaatctcttgcattagttcttgtcaat-tgaccctaa--aaactcatgcttctgtttgactagttttggctctcaagcatctgaatctttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
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gtgagatctctgcttgtgcagagttaagataaccccaatgaaagtttagccatgtctctcttgattatgtaaactgatcttcttgttaatcgctccctgccattttgcagATGGTGGGTGATTTCTTTGACCAATTGAAGTCGAGAACCAAGGGATATGCTAGCATGGAATACTCCGTTATTGG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 16
gtaatctcttgcattagttcttgtcaattgaccctaaaaactcatgcttctgtttgactagttttg-gctctcaagcatctgaatctttttgaatgtc-------aattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
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------------------------------------------------------------gtacagtactctcaagcattttcttctgcttgaatgccgtttaacattttggtagATGGTTGGAGATTTCTTTGATCAATTGAAGTCACGTAGCAAGGGCTACGCGAGCATGGAGTACTCCATTACCGG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 16
gtaatctcttgcattagttcttgtcaattgaccctaaaaactcatgcttctgtttgactagttttg-gctctcaagcatctgaatctttttgaatgtcaatt-------ttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
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------------------------------------------------------------gtacagtactctcaagcatttgcttctgcttgaatgccgtttaaccttttggtagATGGTTGGAGATTTCTTTGATCAATTGAAGTCACGTAGCAAGGGCTATGCGAGCATGGAGTACTCCATTACCGGMapped 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|6134602|gb|AW132995.1|AW132995EST: TGAAAATAGGGCATCAATCACGTATGAATTACCATTAGCAGAG ATGGTTGGTGATTTCTTTGACCAGTTGAAGTCGAGAAGTAAGGGTTATGCT
genomic: TGAAAATAGGGCATCAATCACGTATGAATTACCATTAGCAGAGgtaatctctt ... aattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCT
EST:
gi|120494646|gb|EH222813.1|EH222813EST: TTATTGCTGAAAATAGGGCATCAATCACGTATGAATTACCATTAGCAGAG ATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAAGTAAGGGTTATGC
genomic: TTATTGCTGAAAATAGGGCATCAATCACGTATGAATTACCATTAGCAGAGgtaatctctt ... aattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAA-GTAAGGGTTATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgactagttttggctctcaagcatctgaatctttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
gtttgac putative branch site (score: 4)
aatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctcttgcattagttcttgtcaattgaccctaaaaactcatgcttctgtttgactagttttggctctcaagcatctgaatctttttgaatgtcaattttgtagATGGTTGGTGATTTCTTTGACCAGTTGAAGTCAAGAAGTAAGGGTTATGCTAGTATGGAGTATACCTTTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT