Sequence
atgc intronic sequence ATGC exonic sequencegtaaatctacagcttgttgaacacagctggccattatgcatgtctactcgtaattgatcttctgtaattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG
Basic information
species | Glycine max |
transcript | GLYMA18G01960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 6
----gtaaatctacagcttgttgaacacagctggccattatgcatgtctactcgtaat--------tgatcttctg-taattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG
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gttagtccagctaaccataaccaaatcccattgtttcttatgactatgttgttgtagggttacaggtgcttgccagctaacataaataggattgcagGTTTTGTCTGATGATGAGAAGCGATCAATCTATGATAAATATGGAGAAGCTGGTTTGAAGGGTGCTGGAATGGGAACAGGA
upper sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatctacagcttgttgaacacagctggccattatgcatgtctactcgtaattgatctt----ctgtaattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGG---CATGGGG
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------gtaaagtcctttagatgtgtttttttatcattc-tgctgatacttgaagagcctaaacattgtttttattattttcttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
upper sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 9
gtaaa---tctacagcttgttgaacacagctggccattatgcatgtctactcgtaattgatct-tctgtaattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG
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gtaaaagttcttttgattcatgatttagcttcaacagtttgattgctatctataaaacaattggtttattggcaagctacttgtgcagGTTTTGTCAGATGATGAGAAAAGATCCTTATACGACAGGTATGGGGAAGCAGGACTTAAAGGTGCTGGTATGGGCATGGGGMapped 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|21994326|gb|BQ785854.1|BQ785854EST: AGAACCTGATGCAGAACAGAAATTTAAAGAACTTANTAATGCATATGAA GTCCTGTCAGATGATGAGAAACGATCCATATATGAC
genomic: AGAACCTGATGCAGAACAGAAATTTAAAGAACTTAGTAATGCATATGAGgtaaatctac ... tcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccattatgcatgtctactcgtaattgatcttctgtaattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG
aattgat putative branch site (score: 4)
ttcttttgc putative PPT
taattcaaattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatctacagcttgttgaacacagctggccattatgcatgtctactcgtaattgatcttctgtaattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGGCATGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA