Sequence
atgc intronic sequence ATGC exonic sequence...tatattctcttaactacatgacactgtcggggcttcatagtaatgatttgtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
Basic information
species | Glycine max |
transcript | GLYMA10G38770.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 8
-----tatattctcttaactacatgacactgtcggggcttcatagtaatgatttgtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
||| | | | | || ||| ||| | | | | || || | || | | | | | ||||| |||||||| |||| ||||| ||||| ||||||||||| ||||||||||| || || ||||| |||||| | || |||||||| || | ||||| |
tgttcaatagctacccacccaataagtgctactagggtttctcttcacttgatcagcactcttgttataatg---gttcaagactaaaaaaatttctttc--cagACAGTTCAACAAAATGGATATGAGCAAGACCCTTATGCAAAAGAATTTGGAATCAACATTAGTGAGAAGCTAACCTCAGTTGAAGCTCGGGTCCTTCCTG
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 8
tatattctcttaactaca--tgacactgtcggggcttcata-gtaatgattt--gtttattttatt-tttatttgtatgtggtggtggtgggggtcat--accaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
| ||| |||| | | | | || ||| || ||| ||| || || | ||| || ||| | || ||||| ||||| || |||| |||||| |||||||| ||||| ||||||||||| || || || ||||| |||||| | ||||||||||| ||| | ||||| |
--------cataaatacagctaggatttttcactttttataagtgatggttttaattaatcaaaagatttgttaaaatggctcaagaaacaacattatttgttttcagACAGTTCATCAAAATGATTATGAGCAAGATCCATATGCGAAGGAATTTGGGATCAACATTAGTGAGAAGCTAACCTCTGTTGAAGCCCGAGTCCTTCCTG
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 8
tatattctcttaactacatgacactgtcggggcttcat-agtaatgatttgtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
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-gtatttttttagtcatgtatcttatatggttctttgtgagttagaacttag--aagtgaggatta-----atcttgttgtcaaaaatgttttat----agACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
upper sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 8
--tatattctcttaactacatgacactgtcggggcttcatagtaatgattt-gtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
| | ||| | |||||| |||| | | || || || ||| |||| || | || | |||| | | | | | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || |||||||||||||| ||||||||||||| || || |||||||| |
tgtttgatcttggattgacatgattctgt-gatgtttttgggtcttggtttagtttgagctaataacatct-tatgctttt-taaacttcaaaaaataaccagACGGTTCAACATAATGCTTATGATCAAGATCCATATGCAAAGGAGTTTGGGATCAAAATCAGTGAAAAATTAGCTTCTGTTGAGGCTCGGATTCTTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
tttattttatttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatattctcttaactacatgacactgtcggggcttcatagtaatgatttgtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - -acatgac
- - - - - - - - - - - - - - - ggcttca
- - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggg