Sequence
atgc intronic sequence ATGC exonic sequencegttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
Basic information
species | Glycine max |
transcript | GLYMA05G08750.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttg---cagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
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--------------------------cttacaagttttggtaattgcacatttacatttgtacctat----gtgcatcacgtgttg---acgtttacattttaattga-attgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
upper sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G077125_T01 (Zea mays), 3'ss of exon 5
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
| | | | | ||| ||| | | || |||| |||| | || |||| | | || | || | |||| | | | || | |||||| || |||| ||||||||||| || || || ||||| |||||||| |||||||| ||||| ||||| ||||| |||||||| | || || || ||
------------gaatctcagtccagtttgtttcacttcatatgtgcttgc-gggtccttt-----cggt--cagaattcacataaaaataatgga----gcatttcatgttttctttaca-------cagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTATGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
upper sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
|| | | | | ||| ||| |||| | | |||| ||| |||| | | | | || ||| | || |||| || || |||||| || |||| ||||||||||| || || || ||||| || ||||| |||||||| ||||| ||||| ||||| |||||||| | || || || ||
-----------cttagtccagtttgtttcattttatctgtg-cttttgtg---ggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttct----------------ttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
upper sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 7
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
|||||| | | || | | || || ||| | | | || | || | ||| | ||| ||| |||| | ||| | | || ||||| ||| || || ||||| ||||| | ||||||||||| ||||||||||| || ||||| || |||||||||||||| ||||| | || | ||| |||
----------------------gtatttatataat-ccaaatcctcccagtcctgta---aaacaaatg-attaaattatgt------gacttgatgattatattagctaatacgatttgagatc--acagGGCGGTCGTAAACTATGATTTCCCCAATGGAGTGGAAGACTATGTTCATAGAATCGGAAGAACAGGAAGAGCTGGAGCGACTGGTCAGGCATTCACATTC
upper sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
|| | | || | || | | | || | | || || | |||| | | | || ||||||||| ||||| ||||| || || | ||||| || |||||||| ||||| |||||||| ||||||||||||||||| || || ||||||||||| |||
-----------------------------------------------gtat-gaatatgattccagtttcaaattcaaccatcagaattatagaagcatatgatccg--aatgtagaaatttgattcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC
upper sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgt-tgggtactttaccca--ctgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatatt-ttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
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-----------------------------------gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
atttgac putative branch site (score: 4)
accataaatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgttgggtactttacccactgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatattttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
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