Sequence
atgc intronic sequence ATGC exonic sequence...ttttcagatcaataaaatttctctctctctctctctctctgaaatttctctttctctcagaaattcttcactttccaagtaacatcatgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
Basic information
species | Glycine max |
transcript | GLYMA16G24450.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 5
-----ttttcagatcaataaaatttctctctctctctctctctctgaaatttctctttctctcagaaattctt-----cactttccaagtaacat--catgttttat-tctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
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gtaattgttttacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G36280.1 (Arabidopsis thaliana), 3'ss of exon 5
---------ttttcagatcaataaaatttctctctc-tctctctctctctgaaatttctctttc---tctcagaaattcttcactttccaagtaacatcatgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
|| | |||| || | ||| | ||| || || || | | | | | | || || ||| | | || ||| | ||||||| ||||| |||||||| |||||||||||||| || ||||||| ||| ||||| ||||| | | | | |||
gtaattgttttacttagttaatatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtctctaaccag--agcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02740.t01 (Vitis vinifera), 3'ss of exon 5
---------ttttcagatcaataaaatttctctctctctctctctctctgaaatttctctttctctcagaaattcttcactttccaagtaacatcatgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
|||| | || || ||||||| || | ||| ||| | || | | ||| | ||||| | |||||| | || | ||| |||||| ||||| |||||||||||||| ||| |||||||||||||||| ||||||||||| || ||| | | | |
cttgaaaaattttgatatttattaaatttc---cttgatttctactcctggagctt-tgaatatctgtgctgttcttga--ttccaaagggtgt---gtatatttccagATGGTAATGGGTTCAAGACTAGTACAATGCGACTGGGTGCTGATGTAATTGTTTTCAGCCGTGCATCTCGTACGAG
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S79_35V6.1 (Physcomitrella patens), 3'ss of exon 1
-ttttcagatcaataaaatttctctctctctctctctctctgaaatttctctttctctcagaaattcttcactttccaagtaacatc-atgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCG--GGCAATGCATTCAGG-
| || | || | | | | | | || | ||| | | | | | | | | | | | | ||| || | | | ||||||||||||||||||||| ||| |||| | || ||||| || ||||||||||| | ||| || | | |||
gtcttgaaggatatggagtagcctcgtgtgaatatcatcttacggattccttctgttccttca--tttagagtggtggatttatatctgtgctgtgtggcagATGGCAATGGATTCAAGACCAGTGTCATGCGCCTCGGTGCAGACGTTATTGTTTTTACTCGCCAGCCAAATAACAAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctttctctcagaaattcttcactttccaagtaacatcatgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
aagtaac putative branch site (score: 2)
ttttattct putative PPT
atgttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttcagatcaataaaatttctctctctctctctctctctgaaatttctctttctctcagaaattcttcactttccaagtaacatcatgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - aataaaa
- - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcatg