Sequence
atgc intronic sequence ATGC exonic sequence...tgccactgggacaatgcatgttccaattgctttatttccatgtaagtgtcaagatttacatgactttttaatgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
Basic information
species | Glycine max |
transcript | GLYMA15G16270.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
------tgccactgggacaat--gcatgttccaattgctttatttccatgtaagtgtcaagatttacatgactttttaatgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
||| | | || ||| ||| || || | ||| | | | |||| ||||| | || | |||| | | | |||||||| ||||||||| | ||||| || || |||||||| |||||||| ||||| | || || || ||||||| |||| ||||||||||||||| | ||
ttatcacatgacttgaaaaagcaaaatgagtcaaaaactagatggct-cataaaaaccgacagttac-tgactgtctactctgaattttggtaatt------atgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 7
tgccactgggacaatgcatgt----tccaattgcttta---tttccatgtaagtgtcaa--gatttacatgactttttaatgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
| | ||| | | | || ||| | || | |||| | ||| | | || |||||||| | |||| |||||| || |||||||||||||||| | ||||| || || ||||||||||||||||| ||||| | || || || | | ||| |||| ||||||||| ||||| | ||
gaaaaaaagaacacagaaaatagcatcaaatggattcagactttctttataattacttattatcttggatgactttg------aaattt---tgaattcatttttgcagATTTACATTCTCTTGTACAAGGAAGTTGCTCTTGCTTTGAAAATTAACAGCTTATACAGTAAACAGAGGCTACTTAACATTCATGAAAATGTTAAAGTTC
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------tgccactgggacaatgcatgttccaattgctttatttccatgtaagt-gtcaagatt--tacatgact---ttttaa--tgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
| ||| | |||||| | | || || | | | |||| | || | || ||| ||| || | |||| || | ||| || | ||||| ||||| ||| ||||||| ||||| ||||||||||| || || |||||||| |||||||| | ||||||| ||||||||||||||||| |||||
gtacttactacagaacatgcatgtacttaatagctattatcttctgttgtgaagcatgtctgtagtctgcaatggagatctgacttgtcaggtttggtggattactatctttcaactttttcatttttattactttcttttt-cagATATACATCCTTATCTACAAGGAGGTTGCTCTTGCTTTAAAGATCAACAGTGTATATAGCAAACGCAGGCTTCTTGGCATTCATGAGAATGTGCGGGTAC
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 8
tgccactgggacaatgcatgttccaattgctttatttccatgtaagtgtcaagatttacat-gacttttta------atgcagatttacatgaattttttaa-tgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
| | || || ||| ||| | | ||| | || ||| | || || |||| | | | || || || | | ||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| || || || | ||||||||||||||||||||||||||||| |||
-------gaaatcat-tattcctgcatttttttttctttctgttgattatgggacctactttgatccactagaagggatgctggtgttaatttatcttatgactgcagATTTACATTCTTCTCTACAAAGAGGTTGCTCTTGCTTTGAAAATCAACAGTGTCTACAGTAAAAGGAAGCTTCTTAGCATTCATGAGAATGTGAGAGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtcaagatttacatgactttttaatgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
ttttaat putative branch site (score: 3)
tttttt CT-rich tract
agatttacatgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgccactgggacaatgcatgttccaattgctttatttccatgtaagtgtcaagatttacatgactttttaatgcagatttacatgaattttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATAAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
tgccact
- - - - - - - -gcatgtt
- - - - - - - - - - - -caattgc
- - - - - - - - - - - - - - - - - - -ccatgta
- - - - - - - - - - - - - - - - - - - - - - - tgtcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaat