Sequence
atgc intronic sequence ATGC exonic sequence...aaatattttaataatgtagatgcatttgccggccggaaaacctttttcaataatgcccaattaaattactacagaaactcatttctggcttcaattacagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
Basic information
species | Glycine max |
transcript | GLYMA18G19100.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G19100.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G70460.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------aaatattttaataatgtagatgcatttgccgg-----ccggaaaacctttttcaataatgcccaattaaattactacagaaactcattt-ctggcttcaatta-cagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
|| || ||| | | || | || | || | | | | | ||||| | | || ||| || || ||| |||||| ||| ||||||| |||| |||||||||||| ||||||||| | || || ||||||||||||||||| ||||||||||| ||| | |||||| |||| ||| | |||
gtaagattgatcacaaattctttattaaactactagatatgataaggatgaactagtttgcttgtatacaaaggttagaaggtattacttattgccatatattaataacatctga--gaagtacctaagcctctattttgttggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGAAAGCTGACTGATAGATCAGATGTTTTCTCGTTTGGGGTTGTTCTCTTAGAGCTTATAACAGGACGCAAA
upper sequence: GLYMA18G19100.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G23540.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------aaatattttaataatgtagatgcatttgccggccggaaaacctttttcaataatgcccaa---ttaaattactacagaaactcatttctggcttcaattacagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
||| | | || || | | | | | || || | || | || | | | | ||| | | || | |||||| | || || ||||||||| ||||||||||||| || || ||||| ||||| |||||||| |||||||| ||| | ||||||||||| ||| |||||
gtaagcaaacattcatcacaaactctactccaaaactggaccttattgatccaatgcctgatgaaaagtttgttatatatggcttgaggcaacaaattggatcaaacctgaatctttattgatcgtatggctgcatgacatgttttgtgttaagGTACCTAGCGCCGGAATATGCATCAAGTGGAAAATTGACTGATAGATCCGATGTATTCTCATTCGGGGTTGTTCTCTTAGAGCTTGTAACTGGACGGAAA
upper sequence: GLYMA18G19100.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G70450.1 (Arabidopsis thaliana), 3'ss of exon 4
-aaatattttaataatgtagatgcatttgccggccgga-aaacctttttcaataatgcccaattaaattactacagaaactcatttctggcttcaatta-cagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
|||| | | | ||| | | | | | || || || | ||| | || || || | || || ||||| ||| ||||||| |||| |||||||||||| ||||||| || | || || ||||||||||||||||| ||||| ||||| ||| | |||||| |||| ||| | |||
taaatctgattgtgatgaactagtacgtatagagaggttaagaggttataaattgttgaaaagtacataagcctctaa---tgttataggcttttgttatcagGTACTTGGCACCAGAATATGCACAAAGTGGACAACTTACTGATAGATCAGATGTTTTCTCGTTTGGAGTTGTTCTCTTAGAGCTTATAACTGGACGCAAA
upper sequence: GLYMA18G19100.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0127g00670.t01 (Vitis vinifera), 3'ss of exon 5
----aaatattttaataatgtagatgcatttgccggccggaaaacctttttcaataatgcccaattaaattactacagaaactcatttctggcttcaattacagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
| | ||| || | || |||| || | || || | | | ||||| | | | | | ||| || || | || || |||||||||||| ||||| |||||| ||||||| ||||| || || ||||| ||||| |||||||| ||||| || || | |||||| |||| || | |||
aataagggaaagtaagaaag-agctgcaattcaagatttccaactgttctccta-aatgcatctctgg-tgattgtc-atactaatgtccagtttggctttcagGTACATGGCACCAGAGTATGCATCAAGTGGGAAATTGACTGATAGATCTGATGTATTCTCATTCGGGGTGGTACTTTTAGAGCTTATAACAGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaataatgcccaattaaattactacagaaactcatttctggcttcaattacagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
aattaaattactaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatattttaataatgtagatgcatttgccggccggaaaacctttttcaataatgcccaattaaattactacagaaactcatttctggcttcaattacagGTACATGGCTCCAGAATATGCAACAAGTGGAAAATTAACAGACAGATCAGATGTTTTCTCATTTGGGGTTGTCCTCCTTGAGCTTGTAACGGGAAGGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - aatgtag
- - - - - - - - - - tgcattt
- - - - - - - - - - - - - -gccggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctggc