Sequence
atgc intronic sequence ATGC exonic sequencegtttgatatgagttagagtttgtataatagaatagtaattctttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
Basic information
species | Glycine max |
transcript | GLYMA03G03200.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
gtttg--atatgagttagagtttgtataatagaatagtaattctttttattttttatttttattgtttatttatttatccattattgctat-ttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
|| || || | | | || | || | ||| | | || | | || | ||| | || | | | | || |||||| |||||||||||||| ||||| ||||| ||||| |||||||||| ||||||||| ||||||| | | ||||||||| |||| ||||||||||| ||
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
gtttgatatgagttagagtttg-tataatagaatagtaattctttttattttttatttttatt-gtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
|| || | | | | | | | | | | || ||| | | | ||| | | ||| | ||| ||| | | | | | ||| |||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||| ||||||| | | |||||||||||||| |||||| || |||||
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgt-gcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgatatgagttagagtttgtataatagaatagta-attctttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
| ||||||| ||| | | | | || || | || | || || ||| | | || || | |||| | | | |||||||||||| || || ||||| |||||||||||||| || ||||| |||||||| |||||||| |||| ||||| |||||||||||||||||||||||
-------gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaat-atagcattgcttgtatttgccaacat-gcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtttgatatgagttagagtttgtataatagaatagtaattctttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
| || | || ||| ||| | | | | | | || | ||| | | |||| ||| | || | | ||| | | | |||||||||||| || || || || |||||||||||||| || ||||| |||||||| |||||||| |||| |||||| ||||| ||| | || |||||
gtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctat-----aactgtatttacaattgtgctctctgctttggctgctat-gcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGAAGCATTTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 2
gtttgatatgagttagagtttgtataatagaatagtaattctttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
| | | ||| | | | | | | | | | | ||| || | | || | | |||| |||||||| ||| |||| |||||||||||||| |||||||||||||||||||||||| || |||||||| ||||||||||||| |||||| ||||||||||||||||| |||||
-------gttggctgctgttcct-tgaaacttaattcaatgtctgtatgttagaatgctaataaccggtc-cttatgtgttattgct---tttatagGCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGTTTGGCCGCTGTGGAGAAGCATTTGGCTGCAAGATTCAACAAACCTGACAATGAGATTGTCGACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
ctattttt CT-rich tract
ttttttatttttattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatatgagttagagtttgtataatagaatagtaattctttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA