Sequence
atgc intronic sequence ATGC exonic sequence...cttgagctaggagtaaagatatatatgtttcctttattcgtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
Basic information
species | Glycine max |
transcript | GLYMA08G20100.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 1
cttgagctaggagtaaagatatatatgttt-cctttattcgtaagtagctcccagtcaac--aatggctatctgtttaaaacatgtattgcattttat-tgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
||| | | || ||||||| || | |||| |||| | || | | || | | || | | | | ||| | |||| || |||| || || || ||||||| || |||||||||||||| || ||||| || |||||||||||||| ||||| ||| ||||||| |||||||| |
ctttcctaaaataaattcattattatgtttaccataattccatggtagaactttgtgagctcaacagttctcatct----gccttttatgcttcttatatgcagTACAAAGTTGAAGAACCAGTTAAGCTCTGGGTGAACAAAGTCGGCCCTTACAATAATCCACAAGAAACTTACAACTATCACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 1
cttgagctaggagtaaagatatatatgtttcctttattcgtaa-gtagctcccagtcaacaatggctatctgtt-taaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
|| || | | | | | ||| | | | || || | | | | || | | | ||| | | ||| | |||||| ||| || || ||||| || ||||||||||| ||||| || || ||||| ||||| ||||| ||||| || |||||||| || ||||||| |
-tttaggtgatattttggcctactgtgtattttggaggaagaatgtgtttgtctggtgctttggaacatttacgatgtgtcgtgttcttcgctttgt-gtagTACCAATCGGAGGAGAAGGTTATGCTCTGGGTGAACAAGGTTGGCCCGTACAACAACCCACAGGAAACTTACAACTACTACAGCCTTCCGTTTTGCCATC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 1
--cttgagctagga-gtaaagatatatatgtttcctttattc---gtaagtagctccc--agtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
| ||| | | || | |||| ||||| || | | || || | || | |||| | | ||| ||| || ||| | ||| || |||| || || || ||||||| ||||||||||| |||||||| ||||| |||||||| |||||||| ||||| || |||||||| |||||||| |
gattgctgcttgaatgttgttttccttatgcttcctacatgctgtgcaaatatgttccgtactcaaaatttctcatccctttcaa--------tgcttcttaatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAACAATCCTCAAGAAACTTACAACTACTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
-cttgagctaggagtaaagatatatatgtttcctttattc---gtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttat-tgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
| | | | | |||| ||||| || | | || || | | | || | | || | | | || | | | ||| || |||| || || || ||||||| ||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||||||||| |||||||| |
ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattc-----cttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 1
--cttgagctaggagtaaagatatatatgtttcctttattc-gtaagtagctcccagtcaacaatg-gctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
| | ||||| | ||| | || |||| | | || ||| | ||| ||| ||| | | || | ||| ||| ||||| ||| || || || || | || ||||||||||| |||||||| || |||||||| || || || ||||| || |||||||| |||||||||| |
gcccagcgctagat---aggatttttacgtttttgccaacaagctgtctaatcgttctcatccatgcgctttctttctttctgctgctgtttgttt-attttagTACCAAGCAGCGGAGCCTGTGACGCTCTGGGTGAACAAGGTTGGTCCGTACAACAATCCGCAGGAGACATACAACTACTACAGCCTCCCATTTTGCCATG
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgagctaggagtaaagatatatatgtttcctttattcgtaagt------agctcccagtcaacaatggctatctgtttaa--aacatgtattgcattt---tattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
|| | | | || | || ||| | || | | | || | | || | ||||| | || | | |||| || | || |||||||| || || | || | ||| ||||| ||||||||||| || |||||||||||||||||||| ||||| |||||||| || |||||||||||
----------gaattttggttcttac-tctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 1
---cttgagctaggagtaaagatatatatgtttc-ctttattcgtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
| ||| || | ||| ||| | ||| | | | || || | | | || || | | | || | || || | || ||||||| |||||| | || | || ||||| ||||||||||||||||| || |||||||||||||| ||||| || | |||||| |||||||| |
agacactggctct--gttacagtattcatgaaacacttaactgggaaata--tgtgacttaaacataatattgtataaggaaatcatttttgtttctcctgcagTATCAGACAGATGAGCAGGTGACTCTGTGGGTAAACAAAGTTGGTCCTTACAATAATCCACAAGAAACCTACAACTACTTCAGCCTTCCATTTTGTCACC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 1
--cttgagctaggagtaaagatatatatgtttcctttatt-cgtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
| | | | | | | || || | ||| | | ||| || || || | |||| || | | | | || | ||| ||||||| || |||| || |||| ||||||||| || || ||||| ||||| || |||||||||||||||||||||||||| || || |||||||| |||
atgctacttctgtacttactttctgtaagtagctcaaattacagctcttgcttttgttc--cagatgcactttgtt-aacagttttttaattttgtcttgcagTATCAGCAGAATGAACCGGTTACCCTTTGGGTAAATAAGGTTGGACCTTACAATAATCCACAAGAAACGTACAATTATTATAGTCTTCCATTTTGTCGTC
upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 1
--cttgagctaggagtaaagatatatatgtttcctttattcgtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
|| | || | | | | | | || || | | | | | | | | || || | ||| ||| | || ||||| ||| || || || || || |||||||||||||| || ||||| |||||||| ||||| |||||||| || ||||| || || |||||| ||
ggaacgatcggggtgccatgtcagcacctgcacatggctttgtgatgacgaactgggccgcggttgtgatgggtgaggtccgtgtgttgtgagtg--tgcagTATGGCAAAGGGGATCCGGTGATGCTGTGGGTGAACAAAGTGGGGCCTTACAACAATCCGCAAGAGACGTACAACTACTACAGTCTGCCGTTTTGCAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcccagtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
ttttatt CT-rich tract
tttaaaacatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgagctaggagtaaagatatatatgtttcctttattcgtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - -tgtttcc
- - - - - - - - - - - - - - - - - - - - - - - -ctcccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtat