Sequence
atgc intronic sequence ATGC exonic sequence...gcattgttaaatttggacaaaactatggagtgatctgtcatctttgttctgttattagtgtaattactaatctgaagtgacggatggacacacactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g06490.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g06490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 2
gcattgttaa--atttggacaaaactatggagtgatctgtcatctttgttctgttattagtgtaattac-taatctgaagtgacggatggacacacactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
| ||| | |||| | || || | | | || || | || || | | | | | | || | || || | | | |||| | ||||| || || || | || |||||||||||||||||||| |||||||| | || || ||||| ||||| || |||| |||||| || || ||
-ccttgacagtgattttgtttgaaataaaaaaggttgtga-atgtgagtgctttggtgggcattttcttgcagcatgttttaacttttgaattctt-caccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCTCGCGAAAGTGCACCTTCTATAATA
upper sequence: LOC_Os02g06490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 2
gcattgttaaatttggac-aaaactatggagtgatctgtcat--ctttgttctgttattagtgtaattactaatctgaagtgacggatggacacacactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
| | | |||| |||| || || | ||| | ||| | | | | | | || ||| || | || | | | | |||| | |||||||| || || | || |||||||||||||||||||| |||||||| | || || ||||| ||||| || |||| |||||| || || ||
-tgtcagtgattttgtttgaaaaataaggtcgcaaatgtaagtgcttaggttaggtgggcatttttttgcta-catgttttaactttttaattctt-caccagTGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCACGCGAAAGTGCACCTTCTATCATA
upper sequence: LOC_Os02g06490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
----gcattgttaaatttggacaaaactatggagtgatctgtcatctttgttctgttattagtgtaattactaatctgaagtgacggatggacacacactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
|| || || | | | |||| | | | | |||||| || ||| | || || | || || ||| | ||||| || || ||| |||| ||||||||||| |||||||||||||| || | ||||| ||| ||||||||||||||| ||| ||||| |||||
ttggttgtttttctatgtcagtttgtttttacagtg-tttatacttggaaacatgttat-agcttaagaa--aagttgtttcctttttacttcccaaccttcagCGTGTCTTCATCAGACCTTGTCTCGAAGTGGATGGGTGAAAGTGAGAAGCTAGTATCAAACCTTTTCGAGATGGCCCGTGAAAGTGCTCCCTCGATTATT
upper sequence: LOC_Os02g06490.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------gcattgttaaatttggacaaaa--------ctatggagtgatctgtcatct---ttgttctgttattagtgtaatt--actaatc-tgaagtgacggatggacaca---cactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
| ||| || ||||| ||| || || || | | ||||| ||||| || || ||| | | | ||| ||| || | ||||||||| || || || || | | || |||||||||||||| ||||||||||| || | || ||||| || |||||||||||| ||| || ||||| |||
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctgttattagtgtaattactaatctgaagtgacggatggacacacactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
tactaat putative branch site (score: 1)
ttattagtgtaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattgttaaatttggacaaaactatggagtgatctgtcatctttgttctgttattagtgtaattactaatctgaagtgacggatggacacacactgcagTATATCTTCGTCGGATCTTCTCTCCAAGTGGATGGGAGAAAGTGAGAAGCTGGTGACGAACCTGTTCCAGATGGCCCGTGAAAATGCACCCTCCATTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - ggacaaa
- - - - - - - - - - - - - - - tgatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggac