Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 12
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gtaattttgcatccatccttgtttgtacttttat-tatgtttcagaagtactcgtttt--cctctcatactgtgacctgtcacctgtgttcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 13
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gtaattttgcatccatccctgtttctatttttgt-tatgtctcggaagtacttg------ttgttttcccctcatactgtgacttgtgttcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 11
---gtaatgtattc-catccttgttttgacttatatatttgtttct-taaagacttggtttgatttatttt---ccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gtaacaattcacgcgtacttttgcatccatctctatttctatttttgttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 11
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gtacttttgcatccatctctatttctatttttgt-tatgttttggaagtacttg-------ttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------------------------------gtaatg-tattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttct--tccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gttagtcctggttctcttcgtttcaacatgtctcattaattagaatacataagctaaagttttcttgtatataatgatgatcttcctttattttaccaactcttaccaaatttctatagcatgatcaaggtttttttttcccttgtcta---ctggtttctgttttagTGATCATGAAGGTGGAAATGTTAGTGCTCACGCTGGTCACCTG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------------gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttga--tttattttccctcataccttcacctgggttctt---ccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttc--tttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
----gta-atgtattccatcct-tgttttgacttatatatttg--tttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatca-tataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA
upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
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atctcattattaaatgatctgctgaacgttttttttttttaatatcatttttact--actactt--tttaaatgaatctcactgacagatgtat----gttcaaacagTGATCATGAGGGTGGCAATGTAAGTGCTCATACTGTGCATCTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|3758954|gb|C96653.1|C96653EST: GATGATCCCAAAATGCTCGAGTTGATGCGACTATATGTGACAATCCACAC TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
genomic: GATGATCCCAAAATGCTCGAGTTGATGCGACTATATGTGACAATCCACACgtaatgtatt ... gttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
EST:
gi|38470398|gb|CF954529.1|CF954529EST: GATGATCCCAAAATGCTCGAGTTGATGCGACTATATATGACAATCCACAC TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
genomic: GATGATCCCAAAATGCTCGAGTTGATGCGACTATATGTGACAATCCACACgtaatgtatt ... gttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
gtttgat putative branch site (score: 5)
ttcttcc putative PPT
tttgatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA