Sequence
atgc intronic sequence ATGC exonic sequencegttggtgtggttctgccccctttttcttcattagtagtggaactttagtttgatgatttgtgtcaagtttattttttaatattattattattcagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACGTTCA
Basic information
species | Glycine max |
transcript | GLYMA04G05080.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
--------gttggtgtggttctgccc----cctttttcttcattagtagtggaactttagtttgatgatttgtgtcaagtttatttt--ttaatattattattatt-cagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACGTTCA
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gtgtttcattttgtgctgaacaagcatatgcatttttcttgataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
upper sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 7
------------------gttggtgtggttctgccccctttttcttcattagtagtggaactttagtttgatgatttgtgtcaagtttattttttaatattattattatt-cagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACGTTCA
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gttttattcttatataacttcttttttctcctagcacgccattgttca--agcattaaagttggccccttaaaattctttttttgtttgtttttttttttttttttaaatacagGCATCATCAACATGGAAGATGGCAGGCTCGGATTGGGAGGGTTGCTGGAAACAAGGACCTTTATCTCGGGACATTCAMapped 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|4307200|gb|AI444013.1|AI444013EST: AAAAGCAGCGGGTTTTCTAGAGGTGCTTCAATATACAGAGGGGTCACAAG GCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAA
genomic: AAAAGCAGCGGGTTTTCTAGAGGTGCTTCAATATACAGAGGGGTCACAAGgttggtgtgg ... tattattcagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactttagtttgatgatttgtgtcaagtttattttttaatattattattattcagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACGTTCA
ttttaat putative branch site (score: 3)
atgatttgtgtcaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgtggttctgccccctttttcttcattagtagtggaactttagtttgatgatttgtgtcaagtttattttttaatattattattattcagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT