Sequence
atgc intronic sequence ATGC exonic sequence...ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
Basic information
species | Glycine max |
transcript | GLYMA02G42560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
ttatctgtgtataattgtacaaga---attgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
|| || || | | | | || || | | |||| | | | | || || | | | | | | ||| | ||||||| ||| |||| |||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||||
--atatgc-tacacctatgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
ttatctgtgtataattgtac---aagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
|| || || | | | | || | || | | |||| | | | | || || | | | | | | ||| | ||||||| ||| |||| |||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||||
--atatgc-tacacctatgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
ttatctgtgtataattgtacaagaattgtgatc--tttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA-
|| |||| | || || | |||| | || | || || | ||| | | || || | ||| |||| || ||| |||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||||
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgtt-gtatgtgcttctcatatttgtatgccctccttttgacgcaac-cagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
ttatctgtgtataattgtacaagaattgtgatcttt--ttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
|| |||| | || || | |||| | || | || || | ||| | | || || | ||| |||| || ||| |||| |||||||| ||||||||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||||
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgtt-gtatgtgcttctcatatttgtatgccctccttttgacgcaac-cagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccat-attattt-tgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
|| | | | | | | | | || | | | || | ||| | || | ||| ||||| | | ||||||| | ||||||||||| ||||| ||||| |||||||||||||||||||| || |||||||| ||||| || ||||| ||||| ||||| || |||||
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
---ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
| || | | ||| || ||| || | ||| | | | || | |||||| | ||| |||||| | | ||||||| || |||||||| || ||||| ||||| |||||||||||||||||||| || || ||||| |||||||| ||||| ||||| ||||| || |||||
gtagggttcctgcaccac-gtattagg-ttg-aattaagacatcataacggcagtcatgttg-tatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
---ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggttt--atttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
|| | | | | |||| ||| | | | | | || | | | || || ||| ||||| ||| ||||| || ||||||| || | || || || || ||||| ||||||||||| || || || |||||||| ||||||||||||||||| |||||||| ||| ||||||
ttgttgttt-tacttggttgttgggaaatc----tttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
ttatttt CT-rich tract
tttatttctccatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccatattattttgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- atctgtg
- - - - - - - - - - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -agcctga