Sequence
atgc intronic sequence ATGC exonic sequence...tgttctggatataagtaactacaatttgcaaggtaacgattgacaatgagttaatttatcttgtgcaaattcaaattttatgcctttactttcttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
Basic information
species | Glycine max |
transcript | GLYMA14G39890.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39890.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 6
---tgttctggatataagtaactacaatttgcaaggtaacgattgacaatgagttaatttatcttgtgcaaattcaaattttatgcctttactttcttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
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atagaagcaaactaaaggtttctttgcatgtttgcactttaattgatgctgtgctattcaac--tgagttgtttccctcatgacaacgtt-cctcattatcagCTTTCAAGGAATGTCAGCCAGTCATGTTGGATAATTGATGATGAGAGAATGGGGGAAGCATCAGTTGAG
upper sequence: GLYMA14G39890.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------tgttctggatataagtaactac--aatttgcaaggtaacgattgacaatgagttaatttatcttgtgcaaattcaaattttatgcctttacttt--cttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
| ||| | | ||||| | |||| ||| | ||| | ||||| | |||| |||| ||| | | || ||| |||||| || | ||||| |||||| |||| ||||| |||||||||||||||||||| ||||| || ||||||
gtaagtcactgttttcatgttcttggggcagtgtattgtatttgtaaccttcatttctgtgtaaactgtagtttggtaacaaatgaattcgcagatgaccgagcagatctttaacctcttatcgaggatcaatttcaattg-atggttcgatcttatctttgcagTACTCCAGAAATGTTAGTCAATCACGATGGATTATTGATGATGAAAGAATGGGGGAAGCGTCTGTTGAG
upper sequence: GLYMA14G39890.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 6
-----tgttctggatataagtaactacaatttgcaaggtaacgattgacaatgagttaatttatcttgtgcaaattcaaattttatgcctttacttt--cttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
|| | | | | |||| || ||| || | || || ||| | | | | |||||| || |||| || |||||| | |||||| ||| | ||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||||
tgaaatgatttctcttttca-aactctaacttgaaaag--acaggtgtgtatg---tcactgtcttggtgcaacttgcaattc-atattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgagttaatttatcttgtgcaaattcaaattttatgcctttactttcttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
agttaat putative branch site (score: 4)
tgcctttactttctt putative PPT
aaattcaaattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttctggatataagtaactacaatttgcaaggtaacgattgacaatgagttaatttatcttgtgcaaattcaaattttatgcctttactttcttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
-gttctgg
- - - - - - - - - - - - - tgcaagg
- - - - - - - - - - - - - - - - - - - - - -caatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcct