Sequence
atgc intronic sequence ATGC exonic sequence...tttatggctggctttatatagcctactattatacctgctctaatatcgttaacgatatataaatcagtacgtgatatggtgatacatgtttttgtaccagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g05690.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 2
-ttta--tggctggcttta-tatagcctactatt--atacctgctctaatatcg-----ttaacgatatat-aaatcagtacgt-gatatggtgatacatgtttttgtaccagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
|| | | | | ||| ||| | |||| ||| | | || | |||| | || | |||| | || | | | | | | | |||| | | ||||||||||||| || ||||| || || |||| ||||||||| || ||||| ||||||| |||||||| ||| | ||||| || || || || |||||||
gttcaactcaccaacattaacataattttttatttaatataagtccaaacaataacctcttaattaaatcttaaatttgattgtcgttttaatcaaata-aattttatgc-agTGGTTTGAGGTTCTTGATGGACTCCTCGGGAAGCACTGGAGAAACGTGGGTTTGGCCTTTAACTGCACATTTCTTCTGTTTGGATCTGTTATACAACTGA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 2
---------------tttatggctggctttatatagcctacta-ttatacctgctctaatatcgttaacg-atatataaatcagtacgtga-----tatggtgatacatgtttt-tgtaccagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
||| | || |||| || | || ||||| | | | ||||| ||| | || || | | ||| ||| | | | |||||||||||||| || |||||||| || |||| |||||||| || ||||| |||||||||||||||| ||| | || || || || || |||||||| |
gttccactatcccactttcaaatt--ctaaatattgcatgcttcttatattggtctctgtgcaacttttatatatacttctcaatgtgtctgtgtttaatttaacacaagttctctattgcagTGGTTTGAGGTTCTTGATGGGCTCCTCGGGAAACACTGGAGAAACGTGGGCTTGGCCTTCAACTGCACATTTCTTCTATTTGGATCTGTTATCCAACTCA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 2
-----------------tttatggctggct-ttatatagccta-ctattatacctgctcta-atatcgttaacgatatataaatcagtacgtgatatggtgatacatgttt-ttgtaccagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
| | || | |||||| | || || | | | || | ||| | | || ||| ||| | || | |||| || | | |||||||||||||| || |||||||| || |||| ||||||||| || ||||| |||||||||||||||| ||| | || || || || || |||||||| |
gttccactctcccattctcaaattctaaatattatattgtctctctgcaactttttatatatacttcgatctcaatgtatgtatctatctgtttttaacacttacaacttaactattgcagTGGTTTGAGGTTCTTGATGGGCTCCTCGGGAAGCACTGGAGAAACGTGGGCTTGGCCTTCAACTGCACATTTCTTCTATTTGGATCTGTTATCCAACTCA
upper sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 2
---tttatggctggctttatatagcctactattatacctgctctaa----tatcgttaacgatatataaatcagtacgtga---------tatgg---tgatacatg-----tttttgtac-cagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
| | | |||| | | | | ||| | |||| | | | ||||| | | || | | | || ||||| |||| ||| || || | ||||||||||| || || |||||||| |||||| ||||||||||||||| || || ||||||||||| || | || || || || ||||| || ||||
gtacgtgttctttcttttagaaatcatgaaatttgaggtgcttcagccatttttgttaaaacgagaagaaagaagaggggaaaggggacatatgggcttgattcataagtgattcatgcatgcagTGGTTTGAAGTCCTTGATGGGCTTTTGGGGAAGCACTGGAGGAATGTAGGCCTACTTTTCAACTGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgttaacgatatataaatcagtacgtgatatggtgatacatgtttttgtaccagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
cgttaac putative branch site (score: 3)
tgttttt putative PPT
atatataaatcagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatggctggctttatatagcctactattatacctgctctaatatcgttaacgatatataaatcagtacgtgatatggtgatacatgtttttgtaccagTGGTTTGAGGTGCTGGATGGGCTACTGGGGAGGCACTGGAGGAATGTGGGACTGGCCTTCAACTGCACGTTTTTGCTGTTCGGGTCGGTGATCCAACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - tggctgg
- - - - - - - - - - gcctact
- - - - - - - - - - - - - - - - -cctgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacatg