Sequence
atgc intronic sequence ATGC exonic sequencegtgctaacattaccggccacattgcttgttttcatatatggtttttattctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
Basic information
species | Glycine max |
transcript | GLYMA14G08450.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 7
gtgctaacattaccggccacattgcttgttttcatatatggtttttatt-ctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
||||| || ||| | | || | || ||| | ||||| ||| | | || | | |||| |||||| | | || || | || || || ||||||||||| || || | ||||||||||||||||||||||||| ||||
------gtattac--accctatta--tatcaccactaaccgtccttacaatcagatgtaatgttttatact-tattttcttctatttcagTTTGCTATGCATGAAGATCAGCCATACCACAAATCATGCTACAAAGATTTTTTCCATCCAAAATGTGATGTCTGCAAGAACTTT
upper sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g42820.4 (Oryza sativa), 3'ss of exon 7
gtgctaacattaccggccacattgcttgttttcatatatggtttttattctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
| | | || | || | ||| | ||| | || | | || | |||| ||| | ||| | ||||| | || | |||| || ||| ||| ||||||||||| | ||||||||||||||||||||||||| ||||
--------gtaaagag--acctagcatatttcaacataacatgctttaagtaaatgagataactgacattatccat-tcatttgggaagTTTGCAGTTCATGAAGGTAACCCATACCATCGATCCTGCTATAAGGAGCTTTTCCATCCAAAATGTGATGTCTGCAAGAACTTT
upper sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 5
---------gtgctaacattaccggccacattgcttgttttcatatatggtttttattctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
|| | || | || | | ||| | || | | ||| || | |||| | | ||| || | ||| |||||| |||| || || || | || || |||||| ||||||| ||||| ||| || ||||||||||||||||||||||| ||
gtaactcctttgtttacttattaagcagttatccatgtctgcaagagtaatgttt---ctatgcttatag--tcaaccaatatatg--actat-gcagTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT
upper sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 5
-------gtgctaacattaccggccacattgcttgttttcata-tatggtttttattctgtacttaatgctttgttttatacatattattatt---gcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
||| | | | | || | ||| | | ||| ||| | | ||| || || | || | | ||||| || || | ||| ||| | |||||||||||||||||| ||||| ||||| ||||| ||| || |||||||||||||| |||||||||||
gtaatcagtggctattgtgctatctttatagattgctgcagaagtatcatttgtttgatgtttctactggctaacttgacatatattcttgttcttgtagTATTCTATGAATGGGAATTACCCTTATCACAAATCTTGCTACAAGGAGCACTATCACCCAAAATGTGATGTTTGCAAGCACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatggtttttattctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
acttaat putative branch site (score: 4)
ttaatgctttgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctaacattaccggccacattgcttgttttcatatatggtttttattctgtacttaatgctttgttttatacatattattattgcagTTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA