Sequence
atgc intronic sequence ATGC exonic sequence...taatacatcgattatgcaaaggcaagaaattctcaggttttcaagataagatttgatgttgatgatgatgatgtgtgttgcgatgtgtgacattgaacagGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
Basic information
species | Glycine max |
transcript | GLYMA06G46250.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g33850.2 (Oryza sativa), 3'ss of exon 5
-------taatacatcgattatgcaaagGCAAGAAATTCTCAGGTTTTCAAGATAAGATTTGATGTTGATGATGATGATGTGTGTTGCGATGTGTGACATTGAACAGGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
| | | | | | | | || || || ||||||| | | | | | ||| | ||||| | | || | | ||| ||| ||||| || || || | || | || || ||| | ||||| || || | || |||||||||| |||||||||||||||||||||||||| || || |
catatgtcagtcccttaaagtcg-gaggacagtaagttagaaggtttttt---tccgttgtattcttgtttctgatggaggattttttttt-tctgaaattt--cagGCCAGGGCATACGCGAGAGCGATGAAGGCGACCCTCTTCTTCTCCAGCTCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
upper sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G125507_T01 (Zea mays), 3'ss of exon 5
taatacatcgattatgcaaagGCAAGAAATTCTCAGGTTTTCAAGATAAGATTTGATGTTGATGATGAT-GATGTGTGTTGCGATGTGTG-ACATTGAACAGGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
| | || | || | | ||| ||| | || | | || | | |||| || ||| | | || | | |||| ||||||| ||| || |||| || | || || ||| | ||||| || || || || |||||||||| |||||||||||||||||||||||||| || || |
-tacagctccagagtggagtgttgcgaagttccattcctatcgaaacaatact-aatgtgcgtgtcgatcgctaacaaatgtggtttgtgtgttcccaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
upper sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
taatacatcgattatgcaaagGCAAGAAATTCTCAGGTTT--TCAAGATAAGATTTGATGTTGATGATGATGAT-GTGTGTTGCGATGTGTGACATTGAACAGGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
|| || | | |||| || | || | | ||| | || || || | | | |||| | | ||| |||| | ||||||| ||| || |||| || | || || ||| | ||||| || || || || |||||||||| |||||||||||||||||||||||||| || || |
tacagcactgctgctgcacag-cggagtgttgtgaagttccattcctatcggaaacaatctgtgcg-cgttgattgctaaaagtgatctgtgttcct-aacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC
upper sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
taatacatcgattatgcaaagGCAAGAAATTCTCAGGTTTTCAAGATAAGATTTGATGTTGATGATGATGATGTGTGTTGCGATGTG--TGACATTGAACAGGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
| | | || | | | | | || | ||| ||| | || || | || | | || | |||| | || ||||||||| || || |||||||| ||||| || | ||||| || || |||||||||||||| || ||||||||||||||||| |||||||| || ||||
-atttgcttgacttaggtgggccccttgctcttctaaacatatagacgcattttaaagtc-ataaggagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataagatttgatgttgatgatgatgatgtgtgttgcgatgtgtgacattgaacagGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
tgttgat putative branch site (score: 4)
atttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatacatcgattatgcaaaggcaagaaattctcaggttttcaagataagatttgatgttgatgatgatgatgtgtgttgcgatgtgtgacattgaacagGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC
- - - - - - tatgcaa
- - - - - - - - - - -gcaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga