Sequence
atgc intronic sequence ATGC exonic sequence...ttccttgagctaggagtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
Basic information
species | Glycine max |
transcript | GLYMA12G29120.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 1
-ttccttgagctaggagtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttat-tgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
|| | | | || | || || | || | ||| |||| | | | | | | | | ||| | | |||| ||||||| || || || ||||||| || |||||||||||||| || ||||| || |||||||||||||| ||||| ||| ||||||| |||||||| | |
ctttcctaaaataaattcattattatgt-ttaccataattccatggtagaactttgtgagctcaacagttctcatctgccttttat-gcttcttatatgcagTACAAAGTTGAAGAACCAGTTAAGCTCTGGGTGAACAAAGTCGGCCCTTACAATAATCCACAAGAAACTTACAACTATCACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 1
ttccttgagctaggagtaaagatacgtgcttcctttatttgta-agtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttatt----gcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
|| || | | | | || | ||| | | | | || ||| | | | |||| | ||| || || | | |||| ||| || || |||| || ||||||||||| ||||| || || ||||| ||||| ||||| ||||| || |||||||| || ||||||| ||
----tttaggtgatattttggcctactgtgtattttggaggaagaatgtgtttgtctggtgctttggaac-atttacgatgtgtcgtgttcttcgctttgtgtagTACCAATCGGAGGAGAAGGTTATGCTCTGGGTGAACAAGGTTGGCCCGTACAACAACCCACAGGAAACTTACAACTACTACAGCCTTCCGTTTTGCCATC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 1
-----ttccttgagctaggagtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
| ||||| | | |||||||| || | | | | | | | | || | | | | | | || | ||| ||||||| || || || ||||||| ||||||||||| |||||||| ||||| |||||||| |||||||| ||||| || |||||||| |||||||| | |
gattgctgcttgaatgttgttttc---cttatgcttcctacatgc-tgtgcaaatatgttccgtactcaaaattt-ctcatccctttcaatgcttcttaatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAACAATCCTCAAGAAACTTACAACTACTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
ttccttgagctaggagtaaaga-tacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttat-tgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
| ||| || | | |||||||| || | | | | || | | | | | | | || | | ||| ||||||| || || || ||||||| ||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||||||||| |||||||| | |
-ttgctgattgagtgctgttttctttatgcttcctacatgc-cgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 1
ttccttgagctagg-agtaaagatacgtgcttcct--ttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
|| | ||||| || | ||||| || | | ||| ||| || | | | | || | | || | |||||| |||| ||| || || || || || || ||||||||||| |||||||| || |||||||| || || || ||||| || |||||||| |||||||||| |
-gcccagcgctagataggatttttacgtttttgccaacaagctgtctaatcgttctcatccatgcgctttctttctttctgctgctgtttg--tttattttagTACCAAGCAGCGGAGCCTGTGACGCTCTGGGTGAACAAGGTTGGTCCGTACAACAATCCGCAGGAGACATACAACTACTACAGCCTCCCATTTTGCCATG
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
ttccttgagctaggagtaaagatacgtgcttcct--ttatttgtaagtagcttcatctcaaaatggctatctgtttaa--aacatgtattggattt---tattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
|| | | || | | ||| || ||| | | | || | | || | ||||| | || | | ||| || | || ||||||||| || || | || ||||| ||||| ||||||||||| || |||||||||||||||||||| ||||| |||||||| || ||||||||||| |
------gaattttg-gttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 1
ttccttgagctaggagtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
| ||| | | || | || | ||| || | | | | || || | | | || | || | || | |||||||||| |||||| | || || || ||||| ||||||||||||||||| || |||||||||||||| ||||| || | |||||| |||||||| | |
agacactggctctgttacagtattcatgaaacacttaactgggaaatatgtgacttaaacataatattgtataaggaaatcatttttgtttctcctgcagTATCAGACAGATGAGCAGGTGACTCTGTGGGTAAACAAAGTTGGTCCTTACAATAATCCACAAGAAACCTACAACTACTTCAGCCTTCCATTTTGTCACC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 1
---ttccttgagctaggagtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttat--tgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
| ||| | | | || || || | | | || | || | || | |||| |||| | || ||||| | |||||||||| || |||| || |||||||||||||| || || ||||| ||||| || |||||||||||||||||||||||||| || || |||||||| ||||
atgctacttctgtacttactttctgtaagtagctcaaattacagctcttgcttttgttccaga--tgcactttgtt---aacagttttttaattttgtcttgcagTATCAGCAGAATGAACCGGTTACCCTTTGGGTAAATAAGGTTGGACCTTACAATAATCCACAAGAAACGTACAATTATTATAGTCTTCCATTTTGTCGTC
upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 1
---ttccttgagctagga-gtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
| | | | | || | | | | | || | | | | || | | | | || || | ||| ||| | |||||||| ||| || || || | || |||||||||||||| || ||||| |||||||| ||||| |||||||| || ||||| || || |||||| |||
ggaacgatcggggtgccatgtcagcacctgcacatggctttgtgatgacgaactgggccgcgg--ttgtgatgggtgaggtccgtgtgttgtgagtg--tgcagTATGGCAAAGGGGATCCGGTGATGCTGTGGGTGAACAAAGTGGGGCCTTACAACAATCCGCAAGAGACGTACAACTACTACAGTCTGCCGTTTTGCAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttccttgagctaggagtaaagatacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
ttccttg
- - - - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtat