Sequence
atgc intronic sequence ATGC exonic sequence...ccatgcatagttacatctgcatagtcctgtactgctttgtgacagcaactttatgctttggggttataatttcgttttccatttgactgtgtttggacagAGGCAACCCCCAAGTCGGTGTTGAGACTGATGGGCATGAAAGGTCTCACCTTGTACCACCTCAAGAGCCATCTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47190.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AC233960.1_FGT003 (Zea mays), 3'ss of exon 1
ccatgcatagttacatctgcatagtcctgtactgctttgtgacagcaactttatgctttggggttataatttcgttttccatttgactgtgtttgg---acagAGGCAACCCCCAAGTCGGTGTTGAGACTGATGGGCATGAAAGGTCTCACCTTGTACCACCTCAAGAGCCATCTTCAG
| | | || || || | ||| | | || | | | | ||| || ||| |||| ||| ||||| || |||||||| || |||||||| ||| || | |||||||| |||||||| ||||||||||||||| | ||||| || || |||
tttttttttactgatcatgtattgtatcagatccttttttttctttaattctgg---tcgccattacaacttctgtttcgattgtgctgtgcgcggcaaacagAGGCGACGCCCAAGTCCGTGCTGCGGCTGATGGGAATGAAAGGGCTCACCTTGTACCACTTGAAGAGTCACCTCCAG
upper sequence: LOC_Os02g47190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00300.t01 (Vitis vinifera), 3'ss of exon 1
ccatgcatagttacatctgcatagtcctgta----ctgctttgtgacagcaactttat-gctttggggttataatttcgttttccatttgactgtgtttggacagAGGCAACCCCCAAGTCGGTGTTGAGACTGATGGGCATGAAAGGTCTCACCTTGTACCACCTCAAGAGCCATCTTCAG
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---tgactctttcccttggcattatgtgacaatatctgttcttcataagtaatatgattgttctcttgcaatcaactcaatctttgg--ggttctacatctccagAAGCAACACCCAAGTCGGTGTTGAGGCTGATGGGCTTGAAGGGCTTGACACTGTACCATTTGAAGAGCCATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactttatgctttggggttataatttcgttttccatttgactgtgtttggacagAGGCAACCCCCAAGTCGGTGTTGAGACTGATGGGCATGAAAGGTCTCACCTTGTACCACCTCAAGAGCCATCTTCAG
atttgac putative branch site (score: 4)
ttataatttcgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatgcatagttacatctgcatagtcctgtactgctttgtgacagcaactttatgctttggggttataatttcgttttccatttgactgtgtttggacagAGGCAACCCCCAAGTCGGTGTTGAGACTGATGGGCATGAAAGGTCTCACCTTGTACCACCTCAAGAGCCATCTTCAG
ccatgca
- - - - - - - atctgca
- - - - - - - - - - - - tcctgta
- - - - - - - - - - - - - - - -ctgcttt
- - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - cagcaac