Sequence
atgc intronic sequence ATGC exonic sequence...ctcatactgtaactttttggaataagttggtcttaattatatataaaagaaaggagtaaggggaattagaattacaatgctacttggaaattttgaacagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
Basic information
species | Glycine max |
transcript | GLYMA07G01860.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 3
ctcatactgtaactttttggaataagttggtcttaattatatataaaagaaaggagtaag--gggaattagaattacaa--tgctacttggaaattttgaacagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
||| | || | | || || | | |||| || | | ||||| | || |||| | | ||||| | ||| ||||| || |||||||||||||||||||| |||||||| ||||| | | ||| ||| | || || | ||| ||||||||||| | ||| | | ||||
--------gtagcattcatcacttgtttagtaatcacatcatatcctttgaaagctcagtttatgaatt-gcatgacaacctattctttggacactttc--cagGTAACATCAAGGAAGGATCAGGAGCAGTACTGGGCTGACAAGCAGAGGCCTTACAGATACATTTCGGTGCCAGAATTTGCACAGCGGTTTCAACGGTTCC
upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g03550.t01 (Vitis vinifera), 3'ss of exon 7
ctcatactgtaactttttggaataagttggtcttaattatatataaaagaaaggagtaaggggaattagaattaca--atgctacttggaaattttgaacagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
| ||| | || | | ||| || | | || | | || | | | | ||| |||| | | || |||||||||||||||||||||||| ||||| ||||||||||||| || || ||||||| | || | |||| | || ||||||||| ||||||||| ||||
aaaagtttgtggccttgagtagtaa--tgagcccactttgtttcagtcatcagcccaattgaggcccaatattgatgtatgcaaacaatggaattgtcacagGTTACCTCAAGGAAGGATCAAGAGCAGTACTGGGCAGACAGAAGCAAGCCATACAGATACATACCAGTCTCGGAGTTTGCAAACCGGTTCAAGAGCTTCC
upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 7
ctcatactgtaactttttggaataagttggtcttaattatatataaaagaaaggagtaaggggaattagaattaca--atgctacttggaaattttgaacagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
| ||| | || | | ||| || | | || | | || | | | | ||| |||| | | || |||||||||||||||||||||||| ||||| |||||||||||||||| || ||||||| | || | |||| | || ||||||||| ||||||||| ||||
aaaagtttgtggccttgagtagtaa--tgagcccactttgtttcagtcttcagcccaattgagccccaatattgatgtatgcaaacaatggaattgtcacagGTTACCTCAAGGAAGGATCAAGAGCAGTACTGGGCAGACAAAAGCAAGCCATACAGATACATACCAGTCTCGGAGTTTGCAAACCGGTTCAAGAGCTTCC
upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g03580.t01 (Vitis vinifera), 3'ss of exon 8
ctcatactgtaactttttggaataagttggtcttaattatatataaaagaaaggagtaaggggaattagaatt--acaatgct-acttggaa---attttga--acagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
|||| | | || | || | || | ||| ||||| | | || | || | || ||||| | | || |||||||||||||| ||||||||| ||||| ||||||||||| | | ||| ||||| || || |||| || ||||| || | | ||||||| ||||
----tacttttcccttgt----caaaatcccttttagtatgtataacttttggtactagccttttcttcctttctgtgacacttacttgtgatctgctgtggccacagGTTACCTCAAAGAAGGATCAAGAGCAGTACTGGGCAGATTCCACCGAGCCCTACCGATACGTATCAGTCACCGAATTCGCCACCCTGTTCAAGGCCTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagaaaggagtaaggggaattagaattacaatgctacttggaaattttgaacagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
aattagaattacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcatactgtaactttttggaataagttggtcttaattatatataaaagaaaggagtaaggggaattagaattacaatgctacttggaaattttgaacagGTTACCTCAAGGAAGGATCAGGAGCAATACTGGGCAGACAAAAACATGCCATACCGTTATGTTACAGTGACAGAATTTGCAAACAAGTTCAAGAGATTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
ctcatac
- - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgct