Sequence
atgc intronic sequence ATGC exonic sequencegtgctgtattgttactgaaggagatatattaaattgttgattatgtgtgtatttggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA
Basic information
species | Glycine max |
transcript | GLYMA16G19230.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
--------gtgctg--tattgttactgaaggagat--atattaaattgtt-----gattatgtgtgtattt-ggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA
|||||| ||||||| | | || || | || || || ||| | || || || || | | || | | | || || || | ||||||| |||||||| |||||||| |||||||| ||||| ||||||||||| ||||| || ||||||||| ||| |||| | ||||| || |||| | |
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggca-gtgttagtggcctgacaagtcatctaattgttt--ttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgctgtattgttactgaaggagatatattaaattgttgattatgtgtgtatttggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA
|| | |||| || | | | | | | | || || | | || | | | || || | | | | || | |||| || || ||||| |||||||| |||||||||||||| ||||||||||| | ||| |||||||||||||||| |||| | ||||| || || | || |
-----gtctggttattgt------tctcctctggaagcatctctctagatcttgagtcaatccctctgtc-tcttgcatg-attaactccataaata--tattacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
upper sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 5
---------------------gtgctgtattgt-tactgaa--ggagatatattaa-attgttgattatgtgtgtatttggttacatgatatgccatactatatttatgg-tgttcctggctggt-tactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA
| || || || || | | | ||| | || ||| ||| ||||||| || || || || ||| | | | |||||| || | | || | | |||||||||||||||||||| |||||||| |||||||| | || ||||| ||||| || || |||||||||||||||| |||||| ||||||||||||| ||||
gtgctgctttttttctttttaatagtgcatcgtgtatccatttgaaattatctaaatatttttggttatgtgatgat--ggatatttg-catgtttcaat-cacttatggatggttgtcattgatatcctgtagGAAGCCACTGAACTAGGTAAAAAGGCAAGAGACTTGAAGAAAGCGGCTGATGCGCTCCATCAGGAAGAAAGAAGTGGTTCCAAGGGTAGAAAGTGGCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA
atactatatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgtattgttactgaaggagatatattaaattgttgattatgtgtgtatttggttacatgatatgccatactatatttatggtgttcctggctggttactgtagGAAGCCACTGAACTGGGTAAAAAAGCAAGAGAACTAAAAAAAGCAGCTGAGGCACTACATCAGGAAGAAAGAACTGGTTCAAAGGGTAGAAAGTTTCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC