Sequence
atgc intronic sequence ATGC exonic sequencegttggatatattaaatgagcattgttggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g42330.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 7
gttggatatattaaatgagcattgttggctacacaactttttcacc-ttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
|||| ||||| | ||| | || | ||||||||| | ||| || | || | | | ||||||| || ||| |||| ||| | ||||||||||| |||||||||||||||||||||||||| |||||| ||
gttgtttatatggatc---catctcttaatatattactttttcaacgtttcaatgttccttgtgatcatatatcttgtt-ttatttgaatgtctgctttagAACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTTCTATTTTACATG
upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 7
gttggatatattaaatgagcattgttggctacacaactttttcacc-ttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
|||| ||||| | | | | | ||| ||||||||| ||| || | | ||| | | ||||||| | ||| ||| ||| | |||||||||||| ||||||||||||||||||||||| || |||||| ||
gttgtttatatgcatccatcccttaacacagtacatttttttcaccatttcaatgttcattataatcatatatcttgtt-tcgtttgaatatctgcttcagAACTGAGAGCGCTTTGAAGTTTGGGTGGTTTTTCCTATTTTACATG
upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 9
gttggatatattaaat-gagcattgt-tggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcc--tgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
| | ||| | || || || | || | |||| | | || || | | | || || | | ||| || || || || | || ||| ||||| ||||||||||| ||||| |||||||| |||||||||||
ttcaatcctgcacaatcaaacaaagtgtgcttgcata---ttttgatcattctaatttggttacacccttg-attttgaatttgttccattgttatttttgcagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG
upper sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G07480.1 (Glycine max), 3'ss of exon 8
gttggatatattaaat-gagcattgt-tggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctg--ttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
| | ||| | || | || | || | |||| | | || || | | | || || | | ||| || || || || || || ||||| ||||||||||| ||||| |||||||| |||||||||||
ttcaatcctgcgcaatcaaacaaaatgtgcttgcata---ttttgatcattgtaatttggttacactcttg-attttgaatttgttccattgttatatttgtagGACTGACAGTGCTTTGAATTTTGGATGGTTTTTCTTGTTTTACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
atctaat putative branch site (score: 3)
aaaatatctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggatatattaaatgagcattgttggctacacaactttttcaccttttaaaatatctaatacgctagtgtcttgttcttttttcaatgcctgttacagAACTGAGAGTGCTTTGAAGTTTGGGTGGTTTTTTCTGTTTTACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG