Sequence
atgc intronic sequence ATGC exonic sequence...tcaagtctttggagcatatattttagtgttcacatgctcttctgtacttttcgttttcactataaaatacaaattgtaatgaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
Basic information
species | Glycine max |
transcript | GLYMA13G20980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 3
----tcaagtctttggagcatatattttagtgttcacatgctcttctgtacttttcgttttcactataaaatacaaattgtaa--tgaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
||| | ||| ||| | || | ||| || || || | | || | || | |||| | || ||| || | ||| || || ||||||||||| ||||||||||||| ||| |||||||||| || ||||| || ||||| || || || |||||||| || |||||| ||| || || |
ttactcagcttgttgt--catgggtaatatttttcg-at-cttttttatggttaaattgtttgacagttcataccagttctaaactgtcaaaaaattct--tgcagGTTCTTCTACGAATGCTTCCAGAGTATTATCACCATGTCCGTACCTATGAGAACACACTCATAACTAAGTTTTTTGGCCTCCACAGGGTTAAACCGTCCA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 3
-----tcaagtctttggagcatat-attttagtgttcacatgctcttct--gtacttttcgt-tttcactataaaatacaaattgtaatgacca----------aattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
| | ||| | || | || ||||||| |||||| || | | | | | | || | | | || ||| | ||| ||||||||||||| || ||||||||||| || ||||| ||||||||||||||||| || || || || || ||||| ||||| || ||||| || | || ||||
gtttgtgactacttacatatccaccatctctgttttcacattatcttcttagttttctccatgtctttgcgtagactctttgtccgtctgcccattgagcttccagatttactgtgtagGTTCTTCTGAGGATGCTTCCAGATTACCATCATCATGTGAAGACATATGAGAACACCCTCATTACTAAATTCTTTGGCCTTCACAGAATCAAACCATCAA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 3
tcaagtctttggagcatatattttagtg-ttcacatgctcttctgtacttttcgttttcactataaaatacaaattgt--aatgaccaaattttgaaat--gtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
| | || | | ||| | || || ||||| | | ||| ||| || || || || || | | | | | || || | ||||||||| | ||||||||||| |||||||||| |||||| | | |||| || ||||| || ||||||||||||||||| |||||||| | |||||||
----tttactagaactgaagtttatctaatttttatttccttcttttcctttt-tttgggttaaaagattgaagttctctagtcatcgaagttgtgtttttatagGTTCTTTTGCGAATGCTTCCAAACTATCATCATCATGTGCGGTCCCATGAGAACACACTCATAACAAAATTTTTTGGTCTTCACAGGATCAAACCTTCAA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S311_23V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------tcaagtctttggagc-atatattt--tagtgttcacatgctc-ttctgtacttttcgttttcactataaaatacaaattgtaatgaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
| ||| || || || | || | || ||| | || || | | || || ||| | | ||| ||| |||| ||||||||||| | | ||||| ||| || |||| ||||||||| || || ||||||||||| |||||||| ||||||||||| || | |||| || |
gtgatctagaatatgtccagctttttttttacttcagcttcatatatttgctgctgcaataatgcgtgcggcaactagatctctgaggccgcattatcagtaattttggtatgattattgtgctactctagtgctc-ttatttattttcctttggtttgagtttgtttt----tgtagGTTCTTTTGAATATGCTCGCAGCATACCATCTCCATGTGAAAACTTACGATAATACACTCATCACAAAGTTTTTTGGTCTTCATCGCATTAAGCCATACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttcgttttcactataaaatacaaattgtaatgaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
ttttcactataaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaagtctttggagcatatattttagtgttcacatgctcttctgtacttttcgttttcactataaaatacaaattgtaatgaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
- - gtctttg
- - - - - - -gcatata
- - - - - - - - - - - - agtgttc
- - - - - - - - - - - - - - - - catgctc
- - - - - - - - - - - - - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaatt