Sequence
atgc intronic sequence ATGC exonic sequence...agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
Basic information
species | Glycine max |
transcript | GLYMA08G19380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
------agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----------
|| | || | | | | | |||| || | || | || || | |||| || || |||| | |||| || |||| | || || | | ||||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||||
ccctttcaccctaggct--cataatatcgcgacgacttagcaatgat-atgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgc---agAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT
upper sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 2
------agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
|| | || | | | | | |||| || | || | || || | |||| || || |||| | |||| || |||| | || || | | ||||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||||
ccctttcaccctaggct--cataatatcgcgacgacttagcaatgat-atgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgc---agAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGT
upper sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
-----agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaag--ttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
|| ||| || | | ||| || || || | || || | | || || ||| | | || || ||| | || ||| ||| | || || | | |||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
tgttttaccctagggtgctaa--tagtattccatttt-ttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
upper sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
-----agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagt--tcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----
|| ||| || | | ||| || || || | || || | | ||| | ||| | | || || ||| | || ||| ||| | || || | | |||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
tgttttaccctagggtgctaa--tagtattccatttt-ttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA
upper sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------agtgataaa-ttgccaaatttttgttctgccttatttatttt-tatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----------
|| || | | ||| ||| || |||| |||| ||| | || | | | | |||| | | | | ||||| || | |||||||| | || ||||| || | |||||| ||||| || ||||| |||||||| |||||||||||||| ||| |||| |||||||||||
gtgaatacgacttgagctgtcactggtcataaccttgttttgcattatacgagtcatttgacatagagagagagttgattgctttcggtgctgc-ttatctatctcacatcacatggcttcttagtgctgctcagttttaacatcttgttgttgtgggtggttcagGCGTGTGTCAAGAGGATCCAAGATGATGAGTCTGGCCACAAACATTGCACTGGGCAATATTTTGATTACTGGCATTGTGTTGACAAATGTGTAAGTGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
agaaaagtaattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT
- - - - - tgccaaa
- - - - - - - - - - - - -ctgcctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagtaa