Sequence
atgc intronic sequence ATGC exonic sequencegtacctcggaattttattggcagaaagaacatttcagtattctttttgatcttatgaatttgttgcaaacatttgtatcctgttttcaaaacttcataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
Basic information
species | Glycine max |
transcript | GLYMA08G43500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------------------------gtacctcggaattttattggcagaaagaacatttcagtattctttttgatcttatgaatttgttgcaaacatttg---tatcctgtttt---caaaactt-cataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
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gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatca-tactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacctcggaattttattggcagaaagaacatttcagtattctttttgatcttatgaatttgttgcaa-acatttgtatcctgttttcaaaacttcataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
||| |||| ||| | || | | || ||| || | | | || || || | | || |||||| | ||| |||| ||||| ||||| || ||||| || ||||| || |||||||| || ||||| || |||||||||| || ||||||||||| || || || || || |
---gtacggtattt--ttgtcttggtttactcggctttgtttcaattgggtatac-actgtattataatgcagtcttctcatgttttgggggggtt-------ttgcagGTCGTGACAAGTTTGGCAGACCCATCGGCCAACATCATATTTGGAGCTGTTGTGGATGATCGCTACACCGGAGAGATTCATGTAACGATAATCGCCACAG
upper sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
gtacctcggaattttattggcagaaagaacatttcagtattctttt-tgatcttatgaatttgttgcaaacatttgtatcctgttttcaaaacttcataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
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--atagtggc-tttttttggcacctatcatttgaaattgtccttttgtggggttgtgt-tttcttgcattttcttatg-ctaatatttgcatatccatgatt----cagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCGMapped 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|19348082|gb|BM892614.1|BM892614EST: TTACTGGAGGAAAAGACATAACTCTACAGGAAGTGAACAGAGTGTCTCAG GTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTT
genomic: TTACTGGAGGAAAAGACATAACTCTACAGGAAGTGAACAGAGTGTCTCAGgtacctcgga ... actgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTT
EST:
gi|207833203|gb|GD801842.1|GD801842EST: TTACTGGAGGAAAAGACATAACTCTACAGGAAGTGAACAGAGTGTCTCAG GTTGTGACTAGTTTAGCCGA
genomic: TTACTGGAGGAAAAGACATAACTCTACAGGAAGTGAACAGAGTGTCTCAGgtacctcgga ... actgttgtagGTTGTGACTAGTTTAGCCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaatttgttgcaaacatttgtatcctgttttcaaaacttcataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
tcataac putative branch site (score: 2)
ttttcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctcggaattttattggcagaaagaacatttcagtattctttttgatcttatgaatttgttgcaaacatttgtatcctgttttcaaaacttcataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT