Sequence
atgc intronic sequence ATGC exonic sequence...ctaatacattttggttactcttgcatttatgtctaagatattttattcttatgatttcatctttctataagtaaggcttcatttttcttgtctaatacagGTGATGTAGGTGCTCTGGGCTGGTGGGACTTGTTTATTAATTTTAT
Basic information
species | Glycine max |
transcript | GLYMA05G07960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 6
ctaatacattttggttactcttgcatttatgtctaagatattttattcttatgatttcatctttctataagtaaggcttcatttttcttgtctaat-acagGTGATGTAGGTGCTCTGGGCTGGTGGGACTTGTTTATTAATTTTAT
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gcaaactatcttagattgtacaatattcaggttttt-atttctcttcggcctaattttcctctactctgaaatgttttgtgatattattattgcatgacagGTGATGTTGGTGCTTTGGGATGGTGGGATTTGTTTATAAATTATGG
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G704032_T01 (Zea mays), 3'ss of exon 6
-------ctaatacattttggttactcttgcatttatgtctaagatattttattctt-atgatttcatctttctataagtaaggcttcatttttcttgtctaatacagGTGATGTAGGTGCTCTGGGCTGGTGGGACTTGTTTATTAATTTTAT
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ttttagtttcaca-gcgtcagaagtttctctctctgtctctcaggtctcttttgctttgttgtgcaatgcttttgtaa-taatgcgttgttgcacatg------gcagGTGATGTTGGTGCTTTGGGCTGGTGGGATTTGTTTATAAATTATGG
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 3'ss of exon 6
----ctaatacattttggttactcttgcatttatgtctaagatattttattcttatgatttcatctttctataagtaaggcttcatttttcttgtctaatacagGTGATGTAGGTGCTCTGGGCTGGTGGGACTTGTTTATTAATTTTAT
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gtttctaatttttttaatcagaagttacctttttatgtcata-attccagttttacagtgcactggttttctaatata---ttttttttactataatattgcagGTGATATAGGTGCTCTAGGCTGGTGGGACTTGTTCATAAATTTTGGMapped 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|208240623|gb|GE036009.1|GE036009EST: TATGGTGTTCTTCGTTGCTGCTACAGCCTTCACACTCCTAAAGCTTAGTG GTGATGTAGGTGCTCTGGG
genomic: TATGGTGTTCTTCGTTGCTGCTACAGTCTTCACACTCCTAAAGCTTAGTGgtaactcttt ... tctaatacagGTGATGTAGGTGCTCTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttatgatttcatctttctataagtaaggcttcatttttcttgtctaatacagGTGATGTAGGTGCTCTGGGCTGGTGGGACTTGTTTATTAATTTTAT
gtctaat putative branch site (score: 3)
cttcatttttcttgtc CT-rich tract
tttctataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaatacattttggttactcttgcatttatgtctaagatattttattcttatgatttcatctttctataagtaaggcttcatttttcttgtctaatacagGTGATGTAGGTGCTCTGGGCTGGTGGGACTTGTTTATTAATTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - -ctcttgc