Sequence
atgc intronic sequence ATGC exonic sequencegtgagatatgatccattaataattgcattctttgtctctctctactccagctcttgtttaatgaatgaatgaatgcatgcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
Basic information
species | Glycine max |
transcript | GLYMA14G00470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G00470.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048582_T01 (Zea mays), 3'ss of exon 3
------gtgagatatgatccattaata---attgcattctttgtctctctctactccagctcttgtttaatgaatgaatgaatgcatgcatg-----cagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
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tccagattgtgatagaatcttttatgacagacagcatgcttatatatcgtttgatctggttgcaaacttgcaaatatacttacttttttatctctcccagTGTGTCCCACGACCCTCAAAAGAATATGCAGGCAACATGGTATAACCCGCTGGCCATCACGAAAGATCAAGAAGGTAGACCACTCTCTAAGAAAGCTCCA
upper sequence: GLYMA14G00470.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G35270.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagatatgatccat-taataattgcattc--tttgtctctctctactccagctcttgtttaatgaatgaat---gaatgcatgcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
|| ||| | | | | || | ||| | || || ||||| || | || | | | | | | |||| |||||| ||||| || || ||||||| ||||||||||| ||||| ||||| | |||||||| |||| |||||||| ||||| || || || |||||||| ||
gtaagaaagaaaacttatagttattatgtctatcttatcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgt-tgcagTTTGTCCAACTACCTTGAAAAGAATATGCAGACAACACGGGATAACACGATGGCCTTCCCGGAAGATCAAGAAAGTGGGGCATTCATTAAAGAAACTCCA
upper sequence: GLYMA14G00470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtgagat-atgatccattaataattgcattctttgtctctctctactccagctcttgtttaatgaatgaatgaatgcat---gcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
| |||| || | || || || | | | |||||||| ||| | | | | | ||||||||| ||||| || ||||||||||||||||| || || || || || | |||||||| |||| |||||||| || |||||||| || | |||||| ||
gcatctatccattaagattatcagttcttgctatgtg-gtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
upper sequence: GLYMA14G00470.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S12_321V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------gtg-agatatgatccattaata-attgcattctttgtctctctctactccagctct-tgtttaatgaatgaatgaatgcatgcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
||| ||| | | | || || | || | | || || || | | | | || || | ||||||||||| || ||||||||| |||||||| | ||||| ||||| | |||||||||| |||| ||||| |||||| | || | ||||| || ||
ggtggatagctgtgtagaaagggcaggtctgtatgttctggcgtccgtgtgaaattgtggtaggtccctgctaagtaacatcgtggttgattcggcgcagTGTGTCCGACTACTCTGAAACGGATATGCCGGCAGCATGGCATCTCCCGGTGGCCTTCCCGGAAGATCAACAAGGTGAGTAGGTCGCTAAAGAAGCTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtctctctctactccagctcttgtttaatgaatgaatgaatgcatgcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
gtttaat putative branch site (score: 4)
tttaatgaatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatatgatccattaataattgcattctttgtctctctctactccagctcttgtttaatgaatgaatgaatgcatgcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA