Sequence
atgc intronic sequence ATGC exonic sequencegtgctatatgcttttatagcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggttggctggttatggttgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
Basic information
species | Glycine max |
transcript | GLYMA03G07890.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 5
---------------------------gtgctatatgcttttat-agcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggtt-ggctggttatggt---tgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
||| || || || || | | | | | || || || | || || | |||| | | ||| || | ||||||||||||||||||| ||||| || || ||| ||||||||||||||||| | ||||| || ||||| | |||||| |||||| || |||| || |
gtgcctatattctcacatacttcttttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 3
---gtgctatatgcttttat-agcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggtt-ggctggttatggtt---gcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
||| || || || || | | | | | || || || | || || | |||| | | ||| || || |||||||||||||||||| ||||| || || ||| ||||||||||||||||| | ||||| || ||||| | |||||| |||||| || |||| || |
tttcaattatgagcattcattagaaccatatttttctactacatataattatcactttgaaattttcaatgtggattgagactgaacatattttctgcagGAAGCAACTGAACTAGGTAAGAAGGCTCGGGAATTGAAGAAAGCAGCTGAAGCCCTTCACCAAGAAGAGAAAAGTGGGAAGAAGGGCAGAAAATGGCGCA
upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------gtgctatatgcttttat--agcaggagacatactaaatattgattgaatatgctgtattatatttattgt--gtggt-tggctggttat--ggttg-----cagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
|| | | | ||| | | | || | ||||| | | || | | | | | | ||| |||| || | || || ||| ||||||||||||||||| |||||||| |||| ||| || |||||||||||||| ||||||| ||||||||| |||||||| | ||||| ||||| | | |
gttcatttgtgctggttattgttgtctacttgtcttcatgcaaagcttttctaaagaatacatgtacacttcgggtagttggcagtgttagtggcctgacaagtcatctaattgtttttcagGAAGCAACTGAACTAGGTAAAAAGGCAAGAGATCTAAAGAAAGCAGCTGATGCACTTCACCAGGAAGAACGAAGTGGTGCTAAGGGAAGGAAGTGGAGGA
upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 5
---gtgctatatgcttttatagcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggttggctggttatggttgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
| ||| | | | | | ||| || |||| | ||| || | | | || | | | | ||| || ||||| ||||| ||||| |||||||| |||| |||||| |||||||||||||| ||||||||||||||||||||||||| | ||||| ||||||| || |
gtctggttattgttctcctctggaagcatctctctagatcttgagtcaat-ccctctgtctcttgcatgat-taactccataaatata-ttacagGAGGCAACCGAACTAGGTAAAAAGGCAAGAGAACTAAAGAAAGCAGCTGATGGACTTCATCAGGAAGAAAGAAGTGGTGCTAAGGGCAGGAAATGGCGGA
upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gtgctatatgcttttatagcaggagacatact---aaatat-tgat--tgaatatgc-tgtattatatttattgtgtggttggctggttatggt----tgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
| | ||| | ||| | | ||| | ||| |||| || |||| | || | | | | | ||| ||| || || | || ||||||| |||||||| |||||||| |||| ||| |||||||||| ||||| | || ||||||||||||||||||||||| |||||||| || | ||||
gtgctgctttttttctttttaatagtgcatcgtgtatccatttgaaattatctaaatatttttggttatgtgatgatggatatttgcatgtttcaatcact-tatggatggttgtcattgatatcctgtagGAAGCCACTGAACTAGGTAAAAAGGCAAGAGACTTGAAGAAAGCGGCTGATGCGCTCCATCAGGAAGAAAGAAGTGGTTCCAAGGGTAGAAAGTGGCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattgaatatgctgtattatatttattgtgtggttggctggttatggttgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
tattgat putative branch site (score: 3)
aatatgctgtattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctatatgcttttatagcaggagacatactaaatattgattgaatatgctgtattatatttattgtgtggttggctggttatggttgcagGAAGCAACTGAACTGGGTAAAAAAGCAAAAGAACTGAAGAAAGCAGCTGAATCACTTCATCAGGAAGAAAGAAGTGGTTCGAAGGGTAGGAAATTTCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT