Sequence
atgc intronic sequence ATGC exonic sequence...ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
Basic information
species | Glycine max |
transcript | GLYMA17G03880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g19690.1 (Oryza sativa), 3'ss of exon 10
----ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
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catttgggtatagcgataaaaattttatcctaag--aatg-cactgttcaggcaaaagttatatcaccgctgttgctaatatttttaaaacatgaattg-acagCTTTGTATTGTCATTGGCTGATGTTGATGCTGAGCTTCTGATGGAAGAGGAAAATCTTGTTTGGACAAGCAAAGATGTTGTCATTGTACTTGAGCATAAC
upper sequence: GLYMA17G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 10
-------------------------------------------ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaacc-aattcaaactgaaatttctaaatgtaatgcttttactatgta-------gCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
| | | || || | | | | || | | ||| || |||||| ||||| || || | |||| | | ||||| || || | ||||| |||||||||| | ||| ||| | | ||| | ||||| || || ||| | || |||||||| ||||||||||| ||||||||||||||| |
gtaagcttcatttacatggacaggcacctcttcctcctctatctctccatctctagcagaacatggttataaa---atcaaactatcatgcctcaaaatttaattctgacaatgatcta-aaatttgaccctttttcttaataaccttcagTTTTGTATTATCACTGGCCGGTGTCGATGCTGAACTTCTCATGGAAGAGGAGAGTCTTGTTTGGACAAGTAAAGATGTTGTTATTGTGCTTGAGCATAAC
upper sequence: GLYMA17G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 10
--ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
| | || | | | || | || | | | | | || | ||| |||| ||| || | | | | || |||||||| |||||| |||||||||| |||||| ||||||||||||| ||||||||| | ||||||||||| || |||||||| ||||||||| ||||||||
ggtgtttatctgcactgctctattatgttgcgtcagctgtgaagtgtatggttttattca--ttaaaatgaatattcaaatgccacaaggtctcttttgcagCTTTGTTCTATCATTGGCTGATGTCGATCCACACCTTATGATGGAAGATGAAAGTCTTGTATGGACAAGTAATGATGTTGTCATTGTGCTTCAGCATCAA
upper sequence: GLYMA17G03880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00200.t01 (Vitis vinifera), 3'ss of exon 4
--ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
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ggtgtttatctgcactgctctattatgttgcgtcagctgtgaagtgtatggttttattca--ttaaaatgaatattcaaatgccacaaggtctcttttgcagCTTTGTTCTATCATTGGCTGATGTCGATCCACACCTTATGATGGAAGATGAAAGTCTTGTATGGATAAGTAATGATGTTGTCATTGTGCTTCAGCATCAAMapped 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|298189397|gb|HO037800.1|HO037800EST: AAGAAACAAGGGGATCTACAACCAACATATGGAACTAGAGTAATTCCTGT CTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGAT
genomic: AAGAAACAAGGGGATCTACAACCAACATATGGAACTAGAGTAATTCCTGTgtgcgtacac ... tactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGAT
EST:
gi|254348906|gb|GR852585.1|GR852585EST: A-GAAACAAGGGGATCTACAACCAACATATGGAACTAGAGTAATTCCTGT CTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGA
genomic: AAGAAACAAGGGGATCTACAACCAACATATGGAACTAGAGTAATTCCTGTgtgcgtacac ... tactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
ttctaaa putative branch site (score: 2)
cttttact putative PPT
aaatttctaaatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctgaatgaagaagtattttgatcggtgttgatgatattattttgattcaaaaccaattcaaactgaaatttctaaatgtaatgcttttactatgtagCTTTGTGCTATCACTGGCTGATGTTGATCCAAACCTTATGATGGAGGATGAAAGTATGGTATGGACAAGCAAAGATGTTGTAATTGTGCTTGAGCATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tgctgaa
- - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - caaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaatgc