Sequence
atgc intronic sequence ATGC exonic sequence...ttaattctatccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
Basic information
species | Glycine max |
transcript | GLYMA08G27740.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 4
-ttaattct--atccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
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tgtaattgtgcattatcttttcaatttcaatatcacacacacgcacaaaggtctcatcttt---tcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G055917_T02 (Zea mays), 3'ss of exon 4
ttaattctatccatttcttaatgctagaaatgt-ttcttcacatcaacattt---gaactaggagtttaccca---cttattctg--tatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
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---------ttagctttttaattttgcaattttcttattcaatttagcatataacaaaaaaagggataatcaataccttttcctgataacatagtctacctcattttagCTGGATGTTTGGGCCAAGGAAAGAGAAGTTGCAGGACTAAAGGCAAGCTTGAGTACACTTACATCTGAGGTACAACGTTTGTATAAGTTATGTGCTGAGT
upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 4
-----ttaattctatccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
|||||||| ||||| | || | | || | || | || |||| | | | | || || | | | | | | | | ||||| | || |||||||||||||||||||||||||| || ||||||| ||||| | ||| | | ||||| ||||||| ||| |||| || || || |||
gctctttaattctg--cattttcttattcaatttatcatataacaaaaaaaactttggatgatcaat--acttttttgtgata-acgtagtctacctcattttagTTGGACGTTTGGGCCAAGGAAAGAGAAGTTGCAGGACTAAAGGCGAGCTTGAGTACACTTACATCTGAGGTACAACGTTTGTATAAGTTATGCGCTGAGT
upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 4
ttaattctat--ccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatatttt-ttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
| | || | |||| | | | | ||| | || | | | | ||||| ||| | || || || | | || | ||||| |||| ||||||||||||| ||||||||| | ||| |||||||| || || | |||||||||||||| |||||||||| ||||| || |
---actgcatgactgattctcagttatcattaaagttcattttatgtttaatatatatgctgatttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAA
upper sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0083g00990.t01 (Vitis vinifera), 3'ss of exon 4
ttaattctatccatttcttaatgctaga--aatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatattttttcca-------tgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
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-------tatccatctcatgcttgaaagttaatgtagcct-gcatctat-tcttcctcatgtatatgctgatttgttttgtaagtattctctggttcatctttgtgcagTTGGAGGTATGGGCAAAGGAAAGAGAGGCGGCTGGATTGAGAGCAAGTTTGAATACCTTGATGTCTGAAGTGCAACGCTTAAATAAATTATGTGCAGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttgaactaggagtttacccacttattctgtatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
ttttttccat CT-rich tract
ttattctgtatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattctatccatttcttaatgctagaaatgtttcttcacatcaacatttgaactaggagtttacccacttattctgtatattttttccatgtgtttagCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAATACCTTAATGTCTGAAATACAACGCTTGAATAAATTGTGTGCCGAGA
- - - - - ccatttc
- - - - - - - - -ttaatgc
- - - - - - - - - - - - - - - - - - - cacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgta