Sequence
atgc intronic sequence ATGC exonic sequence...tgaggaaatatgcttttatgttcccgatctctaaggtttccttgctacacttctctataacaccactaacattttttttgtctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
Basic information
species | Glycine max |
transcript | GLYMA04G42670.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g49110.2 (Oryza sativa), 3'ss of exon 7
tgaggaaatatgcttttatgttcccgatctctaaggtttccttgctacacttctcta-taacaccactaa--cattttttttgtctctttaa-------tttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
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-------gtctgtctcttctctagttctctttatattctgttttttatcttgatcaagtaccttcacaagtgcaatagttgagtaacatagaaactgtctgtctcaatagGCACGTGCTGGTGCTGATGTAGTTAGCCCTAGTGACATGATGGATGGCCGTGTTGGAGCAATACGTGCTGCTTTGGATGCTGAGGGTTTCCATGATGTCT
upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g02550.t01 (Vitis vinifera), 3'ss of exon 7
tgaggaaatatgctttt-atgttcccgatctctaaggtttcct--tgctacacttctctataacaccactaacatttt-ttttgtctctttaa-------tttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
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-----------actcttgacatttttgttgcttgaaaatgcatattattcaatgctgctatggcctgactagtttgtgattctaccatgttggacctacttttataaacagGCTAAGGCAGGAGCAGATGTTGTTAGTCCCAGTGACATGATGGATGGTCGTGTAGGAGCAATTCGAGCAGCTCTTGATGCTGAAGGCTTTCAACATGTGT
upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S450_21V6.2 (Physcomitrella patens), 3'ss of exon 7
----tgaggaaatatgcttttatgttcccgatctctaaggtttccttgctacacttctctataacaccactaacattttttttgtctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
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caggtcccaagatgtaattcttgattgcataaatactcgtttacgagcgtattcttgtttgtcttcttaatgagatctaagaagg----ttaacttgacctcagGCTCAAGCTGGGGCAGATGTTGTCAGCCCTAGTGATATGATGGATGGGCGTGTAGGTGCCATCCGAAATGCCCTCGATTTAGCAGGATACCACGATGTTT
upper sequence: GLYMA04G42670.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S219_94V6.4 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------tgaggaaatatgcttttat-----------gttcccgatctctaaggtttccttgctacacttctctataacaccactaacattttttttg-tctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
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gtacgggtttcgtgaagaagattacttcattagctcttaatacccttttcctgatgatctcaattctcgtcaagtagagacacatcaaggacccaacaggtcgttaaggtgctcgtttcgaatgttacctggattagatgtgatgaaattgacttgactgcagGCTCAAGCTGGAGCAGATGTTGTTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTTMapped 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|7693203|gb|AW761299.1|AW761299EST: TTATGAATGATGAGACAGTTCATCAGCTATGTAAACAAGCTGTAGCCCAG GCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGG
genomic: TTATGAATGATGAGACAGTTCATCAGCTATGTAAACAAGCTGTAGCCCAGgtcatatgac ... ttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacacttctctataacaccactaacattttttttgtctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
ttttttttgtctcttt CT-rich tract
attttttttgtctctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaggaaatatgcttttatgttcccgatctctaaggtttccttgctacacttctctataacaccactaacattttttttgtctctttaatttacaaaaagGCCCAAGCTGGAGCAGATGTTGTCAGTCCTAGTGATATGATGGATGGTCGGGTAGGAGCACTGCGTGCAGCTCTGGATGCTGAAGGCTTTCAGCATGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - tatgctt
- - - - - - - - - tgttccc
- - - - - - - - - - - - - - - - - - - -ccttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaccac