Sequence
atgc intronic sequence ATGC exonic sequencegtacttcttaattattgaaaactaaacaatttattaattttcctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
Basic information
species | Glycine max |
transcript | GLYMA16G07490.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G07490.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G165231_T01 (Zea mays), 3'ss of exon 4
gtacttcttaattattgaaaactaaacaatttattaattttcctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
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-----------------gtttctactgcatccatatttttagtttctgagtccttaattttctgtattattaatgtaacctgggaattctaaacagTTGTACAGCACAGTAACACTGAGGCATGGAGAAAAGAAGCATTACAACCACAAAGTAGATGTCTACAGCTTTGCAATTGTGTTGTGGGAACTCCTCCACA
upper sequence: GLYMA16G07490.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g09290.t01 (Vitis vinifera), 3'ss of exon 4
gtacttcttaattattgaaaactaaacaatttat-taattttcctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
|||||| | | | ||| | | || | | ||||| || || |||| ||| | || | |||| | || || | ||||||||| | ||||| ||||| || | || || || ||||||||||| |||||| | || |||||||| ||||||||||| || || |||||||| || | ||||
gtactttgt--tcagaaaaatgcatgcttcttttgttattttgcttttctgtgg-ccacttcagaa--ccatgaact---ttgttatctggtggcagTTGTACAGTACTGTGACATTAAGGCATGGAGAGAAGAAGCACTACAACAACAAAGTGGATGCTTATAGCTTTGCCATTGTCTTGTGGGAGCTTTTACATA
upper sequence: GLYMA16G07490.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07184 (Selaginella moellendorffii), 3'ss of exon 4
gtacttcttaattattgaaaactaaacaatttattaattttcctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
| | | | ||| | | || | | || || | | | | | | || | | |||||| |||||||| || || || ||| | || || ||||||||||| || || |||||||| | ||| |||||||| || ||||||||||| || | |
--------------------gtcagatatgctcttatccataatcttccat--tttgtactaaaa---caaaaccttctcttttactccctcgcagCTCTACAGCACGGTGACGCTAAGAAACGGCGAAAAGAAGCATTATAATCAAAAGGTGGACGTCTACAGCTTTGCAATCGTGTTGTGGGAGCTGCTGACCA
upper sequence: GLYMA16G07490.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ09179 (Selaginella moellendorffii), 3'ss of exon 4
gtacttcttaattattgaaaactaaacaatttattaattttcctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
| ||| || | | | | | ||| | | | | | || | | |||||| |||||||| || || || ||| | || || ||||||||||| || || |||||||| | ||| |||||||| || ||||||||||| || | |
-------------------------gtgagatatgctcttatccataatcttccattttgtgctaaaacaaaaccttctcttttactccctcgcagCTCTACAGCACGGTGACGCTAAGAAACGGCGAAAAGAAGCATTATAATCAAAAGGTGGACGTCTACAGCTTTGCCATCGTGTTGTGGGAGCTGCTGACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
tttcatttcttgttt CT-rich tract
atattagtaatttatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttcttaattattgaaaactaaacaatttattaattttcctgttgggtggtccatattagtaatttatgatttcatttcttgtttggtggcagCTTTACAGCACTGTTACTCTGAGACAAGGGGAGAAGAAGCATTACAACCATAAGGTGGATGCCTATAGCTTTGCTATAGTGTTGTGGGAACTCATCCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA