Sequence
atgc intronic sequence ATGC exonic sequence...attctattctctgaaatctgatttgtttaatttttttagcatccaagttgatttttttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
Basic information
species | Glycine max |
transcript | GLYMA01G38580.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
----------attctattc--tctgaaatctgatttgt----ttaatttttttagcatccaagttgatttt-tttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
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gtaattggttattttaagcaaacttgggcttaatgtgaggtattcatttgtttggta--catgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgac--cagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 14
---att-ctattctctgaaatctgatttgtttaatttttttagcatccaagttgatttttttttggtttatg-tatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
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tggattgcttgtctct----tctcatacactccattcttctgaagttggactccagttgaaatcacttgctgatggaggataattca-cattttttggatggcagGGGGCAGTTAATTTTGCTTTAATGATGTCTCAAATGGAAGGAGGTTGCCCAGTTGATTACAACACAATAACAGATCTATTCCTTCAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 15
-----------------attctattctctgaaatctgattt--gtttaatttttttagcatccaagttgatttttttttggtttatgta-tagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
|| || || | ||| | | | || ||| | | ||| | | | |||||| || ||| || | ||| | || || |||||||||||||||| |||||||||||||||||||| ||||| ||||||| || | ||||| || || || || | || ||||||
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaat--ctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 14
attctattctctgaaatctgatttgtttaatttttttagcatccaagttgatttttttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
|| || ||| ||| || | | || | || | |||| || |||||||||||||| |||||| ||||||||||||| ||||| || || ||||||||| || || ||||| ||||| |||
------------------------------------------------gtatagttcgttgtcttactcatggttttcccgtattgatcctctgtc-cagGCGGCCGTAAATTTTGCTCTCATGATGGCTCAAATGGAAGGCGGATGTCCAATGGACTACAACGTTATTACCGATCTTTTTCTGCAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 14
attctattctctgaaatctgatttgtttaatttttttagcatccaagttgatttttttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
|| || ||| ||| || | | || | || | ||||| || |||||||||||||| |||||| ||||||||||||| ||||| || || ||||||||| || || ||||| ||||| |||
------------------------------------------------gtatagttcgttgtcttactcatggttttcccgtattgatcctctgt-gcagGCGGCCGTAAATTTTGCTCTCATGATGGCTCAAATGGAAGGCGGATGTCCAATGGACTACAACGTTATTACCGATCTTTTTCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgatttttttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
tcttgat putative branch site (score: 4)
tactttctt CT-rich tract
atttttttttggttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attctattctctgaaatctgatttgtttaatttttttagcatccaagttgatttttttttggtttatgtatagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - ctctgaa
- - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - gcatcca