Sequence
atgc intronic sequence ATGC exonic sequence...tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
Basic information
| species | Glycine max |
| transcript | GLYMA20G29960.1 |
| intron # | 6 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g13540.1 (Oryza sativa), 3'ss of exon 4
tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttaga-------tatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
|||| | | |||| | | | || | ||| | | | | | | | | | | | ||| ||| || | ||||| || || || || ||||| |||||||||||||| |||||||| || |||||||||||| |||| || |||||||| ||||| || || || || || ||
-----gatgcgtag-aatattgaatcttccaatgata-acaacatttttggtagttcgactattggatacagttagcattaactaattctatttttctatttgacagTATGTCCCACAACCATGAAACGCATCTGCAGGCAACATGGGATTTCTCGTTGGCCATCTCGAAAAATTAACAAGGTCAACCGGTCTCTCTCAAAACTAAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G475305_T01 (Zea mays), 3'ss of exon 4
tttcccccaagtagtagcagcagctc------ttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacat--actgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
||||| || ||| | | |||||| | || | | | | | ||| |||| | | | | || | | ||||||| ||||| || ||||||||||| ||| ||||||||||||| || |||||||||||| |||| ||||| ||||| ||||| || || ||||| || ||
--------gagtagaggcggcaacacagtggattttgcagtggtgtaagtggttgactcttggagattgtgagcattaactggtgtactttttcttggttcctggcagTTTGTCCTACAACTATGAAGCGCATTTGCCGGCAGCATGGGATTTCTCGTTGGCCATCTCGAAAAATCAATAAGGTCAACCGATCTCTCTCGAAACTAAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G176655_T01 (Zea mays), 3'ss of exon 4
----------tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
||| | | | || | || | || | |||| |||| | || | || ||| | || ||||| |||||| || ||||| |||||||||||||| || ||||| ||||| || || || ||||||||| || | |||| ||||||||||||| | | || || | ||
cattcatgtgtttatatttatt--tgatttgagtccattcatgtcatgattgggaaaaaagaaagtcgacacttggatat-----tctaaatcatgtttttt---tacagTATGTCCTACAACAATGAAGCGCATTTGTAGGCAACATGGTATTTCTCGCTGGCCATCTCGACAAATCAGCAAGGTTAACCGTACTGTTTCAAAATTAAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G375675_T01 (Zea mays), 3'ss of exon 4
tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttc-----ttagatatatttttactgta-----cagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
| || | | | |||| | | || || | | ||| || | ||| | || || | |||| | | |||| | || ||||||| ||||| || ||||| ||||||||| |||||||||| || || |||||||||||| | || || || ||||| ||| | || || ||||| | ||
---------ggcagcaaaaagcggatttttcagtggtgataacgatgtaag-gggttgactcttggagattgtgagcattaattagtttcactttttttatatctggcagTTTGTCCTACAACCATGAAACGCATCTGCCGGCAGCATGGAATTTCTCGTTGGCCATCTCGGAAAATTAATAAGGTCAACAGGTCTCTCTCGAAATTAAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G64530.1 (Arabidopsis thaliana), 3'ss of exon 4
tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
| | | || | | | || | || | | | | | | | || | | || ||||| | ||||||||| || |||||||| ||||| ||| | || || ||||| || || ||||||||| |||| ||||||||||| ||||| || || | || ||
-------------------gtatgttcttaactctgtgtactaattgtaattgt-tgataacaaactctaaaaattttgtgctacttttttcc-----agTTTGCCCAACAACAATGAAACGCATTTGCCGACAACACGGGATCTCACGGTGGCCATCTCGAAAAATCAACAAGGTGAACCGATCTCTCACACGACTTAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G24020.1 (Arabidopsis thaliana), 3'ss of exon 4
tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttaga---tatatttttactgt-acagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
| | || | || || || || | | ||| | | | |||||| || ||| ||||||||||| || ||||||||||| || |||||||| || || || || || |||||||| || |||||||| || || || ||||| | | ||||| ||
----------------------gtctatccatttacttttcatgttttggttagttactggct-agagatatttcatctgaactctatattgttcttgtcacagTTTGCCCGACGACAATGAAGCGAATTTGCAGGCAACACGGAATCTCGCGGTGGCCATCGAGGAAGATCAAGAAAGTGAATCGTTCAATCACAAAGCTGAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g02070.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagta-agtagtgtctcaaacatactgttcttagatatatttttactgt-------acagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
|| |||| | | | | || | | | | | | | | | ||| | ||| | | ||||| | ||| || || | |||||||||||||| ||||||||||| || |||||||||||||| || ||||| ||||||||| | ||||||||||||||||| |||||||| || ||||| ||
gtacgtttctacacttaaaaaagttgtttgcaatcttgctctgttatttccaaaatgctgaattaa-tcatctatagaaatcggattgttctattgcaatagcaattgaaatgaattaatcttatcaagattcttgcttttacatttacagTTTGCCCTACTACAATGAAGCGTATATGCAGGCAGCATGGAATCTCCCGGTGGCCATCTCGTAAGATCAACAAGGTTAATCGTTCCCTCTCTAAGCTAAA
upper sequence: GLYMA20G29960.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S109_79V6.1 (Physcomitrella patens), 3'ss of exon 4
tttcccccaagtagtagcagcagctct--------tttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
| | | | | | | | | | || | | | | || | |||| | | | ||| | | | ||| | |||| || || || || ||||||| || ||| ||||||||||||| ||||| ||||| ||| | |||||||||||||| | ||| || ||| |||| | |
------gcgaagaatgggtgtggatttggatgtggtatgggttgcgtgcggggtcaagatgggtaggtgcgtgtagttgatgtggtgtgtggtgggtttg--gggcagTGTGTCCGACGACTCTGAAGCGGATATGCCGGCAGCATGGGATCTCCCGGTGGCCGTCTCGGAAGATCAACAAGGTGAGCCGGTCGCTGAAGAAGTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaaagtaagtagtgtctcaaacatactgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
tttttact CT-rich tract
ttcttagatatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcccccaagtagtagcagcagctcttttgcctagagagaaaaaggaaagtaagtagtgtctcaaacatactgttcttagatatatttttactgtacagTTTGCCCTACCACAATGAAGCGCATCTGCAGGCAGCATGGGATATCCCGTTGGCCATCTAGAAAGATCAACAAGGTTAACCGTTCCCTGTCGAAGCTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
-ttccccc
- - - - - - - -agcagca
- - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacat
