Sequence
atgc intronic sequence ATGC exonic sequence...agattttctgtgtattatatacaaagttcttatatatatgaaattttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
Basic information
species | Glycine max |
transcript | GLYMA02G44980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g43790.2 (Oryza sativa), 3'ss of exon 6
------agattttctgtgtattata-tacaaagttcttatatatatgaaattttggatcaattac-taattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
| | | | ||||||| || |||| | |||| | ||| | | | || | || || |||| | | || | |||| | | | ||||| ||||| || || || || |||||||||||||| || || ||||| |||||||||||||| |||||||| || || || |||||||| |||
ttctttcgtcatgcagagtattatggtagaaaggttttat-tgtatta------gcagcattcacatacttacagtgtaacagaataactgtactttttct-cgccagGCACTTGATACATTTAATACTGCAATTGTATCTCCAATCTATTATGTAATGTTCACAACACTAACAATACTTGCAAGCGTCATAATGTTCAAG
upper sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 6
-agattttctgtgtattatatacaaagttcttatatatatgaaatt-ttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
| ||| | | | |||| | | |||| || | ||| || | || || | | || || | || | || | |||| |||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| |||
acaacgcactgaagtgtgttactagagttaccacaaatattaagctactggttcctgttctgctttatggagtaagtagtggttttttttt--ttgctgtagGCACTTGACACGTTCAACACGGCAATTGTATCTCCAATATATTATGTAATGTTCACAACTCTTACAATACTTGCCAGCGTCATAATGTTCAAG
upper sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g03650.t01 (Vitis vinifera), 3'ss of exon 6
---------agattttctgtgtattatatacaaagttctta-tatatatgaaattttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
||| || | |||| | | | || | | || || ||| |||||| | | ||| || ||| ||| | || | |||||||||||||| || |||||||| ||| |||| || || ||||| ||||||||||||||| |||||||||| || || ||||| |||||||| |||
attcttaaaggatgtttcacttga-atatggattgatgctactggacataaattttctgatcaaaagtt------ttttctctcacaacatttttctga---tgtttcagGCTCTTGATACTTTCAACACTGCAGTTGTGTCCCCCATATATTATGTCATGTTCACATCACTTACAATCCTTGCTAGTGTGATAATGTTCAAG
upper sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 6
------------------------agattttctgtgt-attatatacaaagttcttatatatatgaaatt--ttggatcaattactaattactcttcactgacatgattgtattgtaa---------ttattt---cagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
|| || ||| | | | ||| || | | |||| || | | | || | || | || | | ||| || | | | | | ||||| || ||||| || ||||| |||||||| ||||||||||| || |||||||||||| || | || || || || |||| || ||||| |||
gtaataagcctagcgtgaataaccagcttgaagatgtcactcgaatttaagccagta-aggtgtgaatttggtatgccctctttttgcttgatgttttgaagcgtagttggatcatgaagttggtactcacctgtgcagGCCCTGGACACATTTAACACGGCAATTGTTTCTCCTATATATTACGTCATGTTCACATCATTGACCATCCTGGCGAGTGCTATCATGTTCAAG
upper sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ25462 (Selaginella moellendorffii), 3'ss of exon 6
agattttctgtgtattatatacaaagttcttatatatatgaaattttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG-------
| | ||||| || || || | | | | | ||| | | || | |||||||||||||| ||||||||||| |||| || || || |||||||| |||||||| || | || || | || || || || ||||| |||
-----------------------------------gcaaggcatttt--attcttttcttgc-attgcttgcaatccagatctaaaagc--ttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAGGTGAGAA
upper sequence: GLYMA02G44980.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ22449 (Selaginella moellendorffii), 3'ss of exon 6
agattttctgtgtattatatacaaagttcttatatatatgaaattttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
| | ||||| | ||| || | ||| ||| | | || | |||||||||||||| ||||||||||| |||| || || || |||||||| |||||||| || | || || | || || || || ||||| |||
-----------------------------------gcaaggcattttattcttttcttgcattgcttgcaat--aca-gatctaaaagc--ttcgtccagGCTCTTGACACATTCAACACAGCGGTTGTGTCACCAATCTACTATGTAATGTTCACGACGTTCACGATTGTTGCTAGCGTGATTATGTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
ttatttc CT-rich tract
atgattgtattgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agattttctgtgtattatatacaaagttcttatatatatgaaattttggatcaattactaattactcttcactgacatgattgtattgtaattatttcagGCTCTTGACACCTTCAACACAGCAATTGTATCTCCTATATACTATGTCATGTTCACAACACTTACAATACTAGCCAGTGTAATAATGTTTAAG
- - -ttctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatg