Sequence
atgc intronic sequence ATGC exonic sequence...tcaattatatttttttattaaaagaggaagtgaaagtgcacaatttattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
Basic information
species | Glycine max |
transcript | GLYMA20G11300.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 4
---tcaattatatttttttattaaaagaggaagtgaaagtgcacaatttattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
| | | | || | ||| | ||| || | || ||||| ||| | | || ||| | || | | | ||||| || || || || ||||||||||| || ||||| ||||||||||||||||| |||||| | |||| ||||||| || ||||| || || ||||| ||
tggatattgagaacttctaattttttctatacgtggaaataatgaaagccttttgtatt-agcagcga--ttgacttgcacatgttgcttacatgtttggcagATACTCAACATCAATTTAATGCACGTGAGAGTGACTGGGGTTTCACATCTTTTATGCCTTTGAGTGATCTGTATGACCCAAGTAGGGGCTACCTTGTTAA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 4
--tcaattatatttttttattaaaagaggaagtgaaagtgcacaatttattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
| | | | ||||| || | | | | | || | | | | | || | ||| | | | || | || | | ||||| || |||||||| ||||||||||| || || || |||||||||||||| || |||||| | |||| | ||||| || || || || |||||||||||
tataatatccttattttttttctttagttacattatgtttctcactatttctggaatatttcttttggttgaatctatat--gttggtcccatgtttggcagATACTCAGCACCAATTTAATGCACGTGAGAGCGACTGGGGTTTCACATCATTTATGCCTTTGAGTGACCTATATGACCCAAGCAGGGGCTATCTTGTGAA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 4
--tcaattatatttttttattaaaagaggaagtgaaagtgcacaattt-attttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
|| | |||||||| | | | || | | || || |||| ||||| || | ||| | ||| || || || || | ||||||||| || ||||||||||||||||| |||||||||||||||||||| ||||| ||||||||| ||||| | || ||||| |||| || | ||||||||
tgaagatggttgttttttatccttatttgccaaagacatgtatagttggatattgggtttattta-aattttgtgatggct--atctttcttgcattctgcagACACTCAACACCAGTTTAATGCACGAGAAAGTGATTGGGGTTTCACTTCTTTTATGCCTCTTAGTGAACTATACGATCCAGGTAGGGGTTTTCTTGTGAG
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
----------tcaattatatttttttattaaaagaggaagtgaaagtgcacaatttattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
| |||| ||||| || | | | | || || || | || || | || | | ||| | | | | | || | |||||| || || || ||||| ||||| || |||||||||||||||||||| || |||||||| || ||| || ||||||| | ||| | ||| |||||
gagaggattcttaattgtatttattg--tgacaaacgatttg---gtttgtggtgaggttgggggat-tccacggtctta-tatttcccatggcgaccta---tttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------tcaattatatttttttattaaaagaggaagt------------gaaagtgcac---aatttattttggatttatctatgaccttggtgtagcttaattttatttaca-----ctatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
| ||| |||| | ||| || | || | |||||||| || || ||||| ||| | | ||| || | || | |||||| |||||||| || ||||||| |||||||||||||||||| |||||||| ||||||||| | || ||||| ||||| | |||| | | ||||
gttcgttttgtatgcctccatcctctgcaagcgtttctctttgcagatgcaatgggcgttggaaatggtttatttgcttttgtcattctcggacgtggtcgtagttttgttggaagtgcacttaaagacatgttggagcagaatattgtgtaacagcggctgaagggcacgtatgacttcttttgcagATACACAGCATCATTTTAATGTACGCGAAAGTGATTGGGGATTCACATCGTTCATGCCTTTACCAGACTTGTACGATCCATCTCGAGGTTTCTTGATGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
gcttaat putative branch site (score: 4)
ttaattttatttacac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaattatatttttttattaaaagaggaagtgaaagtgcacaatttattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA
- - - - - - - - - - - - - - - - - - tgcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttggtg