Sequence
atgc intronic sequence ATGC exonic sequencegtttgtggtgtgccgtgatatgttctttttatatttacatatcatgctgtttgtactgtgatctttagttttcatcctttctgctagtctaatactgtcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
Basic information
species | Glycine max |
transcript | GLYMA09G29970.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 4
--gtttgtggtgtgccgtgatatgttctttttatatttacatatcatgctgtttgtactg--tgatctttagttttcatcctttctgctagtctaatactgtcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
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gtattactagctagc--taataggatccagtaatggtgattaatgtttttactctcagtaaatggacacaatataccaatttttgtgacaat--aat----tgattttccttttgcgtaccctttctgcagTCAATAGCTATTCAGTGTTTGGAGGCACTGCAGTTTTTGCATGGACTTGGTCTTATACATTGTGATCTGAAGCCGGAGAACATATTGGTAAAGAGCTACA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttgtggtgtgccgtgatatgttctttttatatttacatatcatgctgtttgtac-tgtgatctttagttttcatcctttctgctagtctaatactg--tcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
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------------------------------------------------gtttgtccactttatcattaccatacatcatagatatgtatatgtatccgattcctgatctctttgggaccgttctgtacagTCAATCACTATCCAGTGTCTCGAATCACTTCAGTTTCTACATGGCCTTGGACTTATACACTGTGATTTGAAGCCTGAGAATATATTGGTGAAAAGCTATA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 10
gtttgtggtgtgccgtgatatgttctttttatatttacatatcatgctgtttgtactgtgatctttagttttcatcctttctgctagtctaatactgtcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
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----------------------------------------gttatggagttacatttttaaact--gatatctttctctcctactgacatgctggtatgtaacctgcttttaaattgttctgtgcagTCCATTACAATTCAGTGTTTGGAGGCACTTCAGTTCTTGCATGGCCTAGGCCTTATACATTGTGATCTGAAGCCTGAGAATATTTTGGTGAAGAGCTATAMapped 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|151404434|gb|EV274248.1|EV274248EST: TTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAAGGTTGCAG TCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGA
genomic: TTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAAGGTTGCAGgtttgtggtg ... atgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcctttctgctagtctaatactgtcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
gtctaat putative branch site (score: 3)
tctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtggtgtgccgtgatatgttctttttatatttacatatcatgctgtttgtactgtgatctttagttttcatcctttctgctagtctaatactgtcataaacacttttcaacttatgtgagcagTCAATTACCATTCAGTGTTTGGAAGCACTTCAGTTTTTGCACAGTCTTGGACTAATACATTGTGACTTGAAGCCGGAGAATATTTTGGTTAAGAGCTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT