Sequence
atgc intronic sequence ATGC exonic sequence...atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os07g08760.2 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124965_T02 (Zea mays), 3'ss of exon 2
atttcctgtcttttcaatgaatctacgtt-tgat---gtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctt-tgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
|| || || | ||||| || ||| || || | || |||| | | | || | |||| | || | | || || | | || |||| ||||||||| |||||||| || ||||||||||||||||||||||| ||||| || |||||||||||||||||||||| ||| |||||||| |||||||
---tcagaagattgcagttaatctgtgtaatgactaaatggtaaatgctttaccata-atttcttcgtata-catcaactgaatttattttaaatgtaattttagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACACCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG
upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G121223_T02 (Zea mays), 3'ss of exon 3
---atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctt-tgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
| || || ||||| || |||| |||| | | ||| ||| |||| | || | || || | || | ||| ||||||||| |||||||| || ||||||||||||||||||||||||||||| || |||||||||||||||||||||| ||| |||||||| |||||||
aacagttagaagattgcagtaaaatctgtgtc----atgactaaatgttttac-cataatatatttgtatacatatcctgagtttattttaaatacatttattagGAGGGACCTATAATGTACTGCAGCCGCACTATTTTTGAGGATGCTACTCCTGAACTGGTTAGAGATTTCTTCTGGGATGGTGATTTTCGTCTAAAGTGGG
upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
atttcctgtcttttcaatgaatctacgt-ttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
| || | || || | | | | || | | | || | | || | ||| || ||||| ||| || | | || | || || |||| | ||| ||||| | ||| | ||||| ||||| ||||| ||| | || || |||||||||||||||||||| ||||||| || ||||
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgt-tggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G23080.2 (Arabidopsis thaliana), 3'ss of exon 3
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
| |||||| |||| | | || |||| | |||| | || | | | || ||| |||| || | || ||| | | || ||||||| ||| |||||||||||| || || || ||||||| |||||||||||||| ||||| ||||| | || ||||
----------------gtaaatctaagttttaaagactctaact------ttatatgacttagttc-----ctgaaaggtgg---ttatgttggttgtcagATAGGTCCTGTTGTTTATCGTAGTCGAACTGTTTTTGAGGATGTAACACCAGACATTGTTAGGGATTTCTTCTGGGACGATGAGTTTCGACCTAAATGGG
upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacat-ctaatggactgatc--ttcctttgcttgt-agGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
| | | | |||||| | | | | | | | || | | | || | | | | | | ||||| | ||| || | || || ||| | || || | || || ||| | ||||||||||| ||||| || ||||||| |||||||||||||||||||| ||||| | || ||||
--gtgttcttgctataatgaaatggggaat--tcttaaatactagatgatagaaacatttgatcaaattgtgtttgtagcctgataggtcgtattgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
upper sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
-------atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
| ||| | | | || || ||| | | | | | | | ||| | | | | | | || || | || |||| || || || | |||| |||| | ||| | ||||||||||| ||||| ||| | |||||||||||||||||||||||||| ||| | | || ||||
gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcatt--agtaaccgataa--tggtgtttctttatc---agAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
gactgat putative branch site (score: 3)
tcttcctttgcttgt CT-rich tract
ttatagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcctgtcttttcaatgaatctacgtttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
