Sequence
atgc intronic sequence ATGC exonic sequence...taaaagaatacttgaccatttattctgtttttttttttttaacttaatattcatgacctctacgtttccatagatttataagattaattttcactttcagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
Basic information
species | Glycine max |
transcript | GLYMA18G46480.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G61250.1 (Arabidopsis thaliana), 3'ss of exon 1
--------taaaagaatacttgaccatttattctgtttttttttttttaacttaatattcatgacctctacgtttccatagatttataagattaattttcacttt-cagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
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tgttccctttggagaaaatt---ccattaactggggttcttcagagattac---atagagaaaagcttta-atctttataactttcttg--tcggtcatggtgaaacagGTTTACTTCGCTGTGGGAAGAGTTGCAGGCTGAGATGGACAAACTATCTGAGACCAGACATAAAGAGAGGTCCTTTCACTGCTGATGAAGAGAAACTTGT
upper sequence: GLYMA18G46480.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
taaaagaatacttgaccatttattctgtttttttttttt---taacttaatattcatgacctctacgtttccatagatttataagattaattttcactttcagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
|| | || || | || | | ||| || | || | ||| | | |||| | | |||| |||||||| ||| | || |||||||| || ||||| ||||||| |||||||||||||| ||||| ||||| || | || ||| ||||| || | | |
-aatgggcagtgagatcaatggaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccat--tctgagtgcgcattttttttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattcatgacctctacgtttccatagatttataagattaattttcactttcagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
gattaat putative branch site (score: 3)
ttttcactttc CT-rich tract
atagatttataagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaagaatacttgaccatttattctgtttttttttttttaacttaatattcatgacctctacgtttccatagatttataagattaattttcactttcagGTCTTCTTCGTTGTGGCAAGAGTTGCAGGCTTAGGTGGACAAACTATCTGAGACCAGACATTAAGCGTGGTCCCTTTACTCTTGAGGAAGAAAAACTAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-aaaagaa
- - - - - - - -ccattta
- - - - - - - - - - - ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - -ttcatga