Sequence
atgc intronic sequence ATGC exonic sequence...agactatataagctgattagtgcttgtattttgaaatcaattaaataatattcagtttgccctttatttcaagtgttacctaattttatgtgcatggaagTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG
Basic information
species | Glycine max |
transcript | GLYMA15G21240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 4
agactatataagctgattagtgcttgtattttgaaatcaattaaataatattcagtttgccctttatttcaagtgttacctaattttatgtgcatgga-agTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG
||| || || || || || | || ||| ||| | || | || |||| || | ||||| || ||||| |||||| |||||||||||||| || | | |||||||||||| || || || | |||||||| || |||||||| | |||||||
-------------------------gtagaggtaacacatttcgtcaaagtt---tctgggcttcatt--gatgagaactctaattcatgtttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGAGTTCCTTAATACCCTTTTCTCTGTTTCAGAAGCTGTCATGTTCATGCAG
upper sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 5
-------agactatataagctgattagtgct-tgtattttgaaatcaattaaataatattcagtttgcccttta-----tttcaagtgttacctaattttatgtgcatggaagTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG
|||| | || ||| || | || | || | || | | | | | || | | | ||| | | ||| | || ||| ||||||||||||||| || || | || ||||||||| | |||||||||||||||||||||| ||||| || || || || || ||| ||||||| |||
gtatatttgacttttcaacaccattggtaatgtgaagaaaaaagagagttgcaaagtcattgttctgttttgaaggaagtctcattctcttattgtctttgtatggatgaaagTGAGATCTATGGAAGGGAGTTAGTTGACCTGCGGAACCAGAGTCGATGGGAGTTTCTCAATACATTTTTTTCAGTTTCAGAGGCTCTGGCTTATGCACAG
upper sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 5
agactatataagctgattagtgcttgtattttgaaat--caattaaataatattcagtttgccctttatttcaagtgttacctaattttatgtgcatggaagTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG
|| || | | || ||||| ||||| | |||| | | || | ||| | | |||| ||| ||| | ||||||| |||||||| |||||||| ||||||||||| ||||| | | |||||||||| || ||||| ||| | |||||||| || ||||| ||||||| ||||||
gtacccta-gattttcccgatgtttgtaatttgatttgctaattgtagcaagactagggtaatattt-tctagagtgcctgttaactttctatgcatggcagTGAGATGTATGGGAGGGAACTGGTGGATCTGCGAAACGAAAGTCGATGGGTATTCCTCAATACACTATTCTCTGTTTCAGAAGCAGTGGCTTTTATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatattcagtttgccctttatttcaagtgttacctaattttatgtgcatggaagTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG
acctaat putative branch site (score: 3)
ttacctaattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agactatataagctgattagtgcttgtattttgaaatcaattaaataatattcagtttgccctttatttcaagtgttacctaattttatgtgcatggaagTGAGATCTATGGGAGAGAACTGGTGGACCTGCGGCAAAAGAGTCGATGGGAGTTTCTCAACACATTCTTCTCTGTGTCCGAAGCTGTGGCTTACATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - -gctgatt
- - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttacc