Sequence
atgc intronic sequence ATGC exonic sequence...tacatcatcttctgtagcttacatttgatatcaaatcatgactgttgatatttaataatgtaatttgtagagatcttaagcactgtttttattgtttcagCCTGCCTTTACAAATTGGAGTGGCGCTCTATCTTTTGTATACTCAAGTCAAATTTGCATTTGTATCTGGATTAGCGATAACCATTTTATTGATACCAG
Basic information
species | Glycine max |
transcript | GLYMA13G44750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G44750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g08560.1 (Oryza sativa), 3'ss of exon 11
tacatcatcttctgtagcttacatttgatatcaaatcatgactgttgatatttaataatgtaatttgtagagatcttaagcactgtttttattgtttcagCCTGCCTTTACAAATTGGAGTGGCGCTCTATCTTTTGTATACTCAAGTCAAATTTGCATTTGTATCTGGATTAGCGATAACCATTTTATTGATACCAG
| | |||| || || | |||| | | | | || |||| | | | ||||| ||| | | | || || | | ||| |||| || || || ||||| || |||||||| |||||||||||||| || | ||||||| |||||||||| || ||||| | || | || ||||
---tcctttttctttatctaatgtttg---cctattaagga--attgactcgtgcca-cattatttgatgagttgtgtggt----ttggcatcttcttagcttgccattgcagATAGGAGTTGCTCTCTATCTATTGTATACTCAAGTGAACTATGCATTTTTATCTGGATTGGCAATAACAGTCATACTAATGCCAG
upper sequence: GLYMA13G44750.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G07680.1 (Arabidopsis thaliana), 3'ss of exon 11
tacatcatcttctgtagcttacatttgatatcaaatcatga-----ctgttgatatttaataatg-taatttgtagagatcttaagcactgtttttat-----tgtttcagCCTGCCTTTACAAATTGGAGTGGCGCTCTATCTTTTGTATACTCAAGTCAAATTTGCATTTGTATCTGGATTAGCGATAACCATTTTATTGATACCAG
||| ||||||| ||| |||| || ||||| | ||| ||| ||| | | | | || | ||| ||||||||||||| |||||||| | || | ||||||||||||||||||||||| ||||| ||| | |||||| | || || ||||| || |||||||||
-------------gtaaga-acatttgcctgtaaacaatgaaagtgcttccaatattgagtaacaataaattggccactcttacaatttttcattcaaatatatgtctcagCCTGCCTTTGCAAATTGGGATAGCTTTGTATCTTTTGTATACTCAAGTCAAGTTTGCTTTTCTTTCTGGACTTGCAATCACCATCTTGCTGATACCAG
upper sequence: GLYMA13G44750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g00310.t01 (Vitis vinifera), 3'ss of exon 3
-tacatcatctt---ctgtagcttacatttgatatcaaatcatgactgttgatatttaataatgtaatttgtagagatcttaagcactgtttttattgtttcagCCTGCCTTTACAAATTGGAGTGGCGCTCTATCTTTTGTATACTCAAGTCAAATTTGCATTTGTATCTGGATTAGCGATAACCATTTTATTGATACCAG
| || | || | |||||| | || || || ||| || | ||| | || | || | | || | || | | | ||||||| ||||||||||||||||| | || || || | |||||||| |||||||||||||| ||||| ||||| | || ||||| || || || |||||||
aaatatttttttgaacaaaagcttataattatcattccatg--gaccatt--tttttcttcatatttttcttcatattttttaattctcatgccaatatttcagCTTGCCTTTACAAATTGGACTAGCACTATACTTGTTGTATACACAAGTCAAATTTGCTTTTGTTTCTGGGATCGCAATAACTATCTTGTTAATACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatatttaataatgtaatttgtagagatcttaagcactgtttttattgtttcagCCTGCCTTTACAAATTGGAGTGGCGCTCTATCTTTTGTATACTCAAGTCAAATTTGCATTTGTATCTGGATTAGCGATAACCATTTTATTGATACCAG
atttaat putative branch site (score: 4)
tttttatt putative PPT
tttaataatgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatcatcttctgtagcttacatttgatatcaaatcatgactgttgatatttaataatgtaatttgtagagatcttaagcactgtttttattgtttcagCCTGCCTTTACAAATTGGAGTGGCGCTCTATCTTTTGTATACTCAAGTCAAATTTGCATTTGTATCTGGATTAGCGATAACCATTTTATTGATACCAG
- - - -tcttctg
- - - - - - - - gcttaca
- - - - - - - - - - - - - - - - - -tcatgac
- - - - - - - - - - - - - - - - - - - - - tgttgat