Sequence
atgc intronic sequence ATGC exonic sequence...acatgtttgtttattccttattttgttgaacaaggtgtaatgttgattgaaaatttggaatgtactatgttttgatgtaagtggcgccttggaaatgcagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACGATGAAGAAAGGTGAAAATTCCCTTTTCACCATCCCGGCTGAGCTAGCTTATGGTGAAACTGG
Basic information
species | Glycine max |
transcript | GLYMA03G21690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------acatgtttgtttattccttattttgttgaac-aaggtgtaat-gttg-----------attgaaaatttg-----gaatgtactatgttttgatgtaagtggcgccttggaaatgcagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACGATGAAGAAAGGTGAAAATTCCCTTTTCACCATCCCGGCTGAGCTAGCTTATGGTGAAACTGG
| | ||| | ||| ||||| || | || | |||| || ||| |||| |||||| ||| |||| || |||| || |||||| ||||||||||||||||||||| ||||||| |||||||||||||||||||| | ||||||| || || || |||||||| ||||| ||| ||||
gtttgtgattctcatctcctaaagacctaatagtttccgtatagttagtaatctggagaattcggtagactaatttgatagatatgaacttgaattgagatatagttgttgttaagttcaaaatcgaatttttgttgatgaatgtgtaatggtttgtggttgttggcattgtgtttttgcagGTCAAGTTATTAAAGGATGGGATATTGGTATTAAGACGATGAAGAAAGGTGAAAACGCTGTTTTCACTATACCTGCGGAGCTAGCATATGGGGAATCTGG
upper sequence: GLYMA03G21690.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G48570.1 (Arabidopsis thaliana), 3'ss of exon 2
-------acatgtttgtttattccttattttgttgaacaaggtgtaatgttgattgaaaatttggaatgtactatgttttgatgtaagtggcgccttggaaatg-cagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACGATGAAGAAAGGTGAAAATTCCCTTTTCACCATCCCGGCTGAGCTAGCTTATGGTGAAACTGG
| | || ||| | || ||||| | | | | | || || ||| || | | ||| ||| | || | |||||| | |||| || || |||||||||||||| || || | || |||||||||||||||||| | |||||||||| || ||||||| || ||||||||||| ||
gtgagagaagttttggttgagagtttgttttgatcgata-gttactat-ttaatta------cggtgtctttcgagttctgaattttgttttggtttggaatggtcagGACATGTCATTAAAGGATGGGACTTGGGGATCAAGACAATGAAGAAAGGTGAAAATGCTATTTTCACCATTCCTCCTGAGCTGGCATATGGTGAAACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaaaatttggaatgtactatgttttgatgtaagtggcgccttggaaatgcagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACGATGAAGAAAGGTGAAAATTCCCTTTTCACCATCCCGGCTGAGCTAGCTTATGGTGAAACTGG
ttttgat putative branch site (score: 4)
tatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatgtttgtttattccttattttgttgaacaaggtgtaatgttgattgaaaatttggaatgtactatgttttgatgtaagtggcgccttggaaatgcagGGCAAGTTATTAAAGGATGGGATCAAGGTATTATAACGATGAAGAAAGGTGAAAATTCCCTTTTCACCATCCCGGCTGAGCTAGCTTATGGTGAAACTGG
- -tgtttgt
- - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcgcc