Sequence
atgc intronic sequence ATGC exonic sequence...ctcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacctctgcttctaattaatgtaaatgatactctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
Basic information
species | Glycine max |
transcript | GLYMA09G05820.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G05820.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G30950.1 (Arabidopsis thaliana), 3'ss of exon 4
------------ctcgttgtcaaaaaaatctttctt-attttcctacgttgcccttctgattacaactttgccacacctc-tgcttctaattaatgtaaatgatactctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
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gtacgcgacacgttcagcttcacattagttatgctggagcctgatgataagtttgatcttttactagttgatgaaactgagtgtttgagactgttgaatatttttactttgcagATGGTAACAACATTTGGAATGTCTGATATTGGACCATGGTCTTTGATGGATTCTTCGGCACAAAGCGATGTCATCATGAGAATGATGGCAAGAAACTCCA
upper sequence: GLYMA09G05820.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G06430.1 (Arabidopsis thaliana), 3'ss of exon 4
ctcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacctctgcttctaattaat-gtaaatgatactcta---gcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
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-------------gtatctcttctacactccca-gcttcagtatttttttctgttatcctaaactagtgaatgaacttgacagtatatcatcatttacttgcagATGGTGACAACATTTGGGATGTCTGAAATCGGACCATGGTCGCTAATGGATTCATCGGAGCAAAGCGATGTCATTATGAGGATGATGGCAAGAAACTCAA
upper sequence: GLYMA09G05820.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 4
ctcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacct--ctgcttctaattaatgtaaatgatactctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTG---ATGTTATCATGAGAATGATGGCAAGAAACTCAA
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cttgctcttttaactaa-ttgcttaacaaataacaatttccctc-acctattatttggacaaatttaactgaatttgacgggtttaataaattcgtttgcagATGGTGACCACATTTGGGATGTCTGACATCGGCCCATGGTCGCTTATGGACACCTCGGCTCAGAGTGCTGATGTCATCATGAGAATGATGGCAAGGAATT---Mapped 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|11687680|gb|BF595356.1|BF595356EST: CAACTGGAGCAGTCGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGCAG
genomic: CAACTGGAGCAGTCGGTGATTTGCAGCAAATAACCAGTTTGGCC-A--AGCAGgttggtgttc ... actctagc
EST:
gi|11274794|gb|BF325129.1|BF325129EST: ACTGGAGCAGTCGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAG ATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGAC
genomic: ACTGGAGCAGTCGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttc ... actctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattacaactttgccacacctctgcttctaattaatgtaaatgatactctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
ttctaattaatgtaaa 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
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ctcgttgtcaaaaaaatctttcttattttcctacgttgcccttctgattacaactttgccacacctctgcttctaattaatgtaaatgatactctagcagATGGTAACCACATTTGGAATGTCTGATATTGGTCCTTGGTCACTCGTGGACTCATCAGCTCAAAGTGATGTTATCATGAGAATGATGGCAAGAAACTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
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