Sequence
atgc intronic sequence ATGC exonic sequencegtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07740.3 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 6
-------gtacgttcctcctatctttta-ctcatctgttatgcgtttttgtgtcctataaagttgat--gtcat-ctaat-tgtacctttttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG
| | || | | | || | | | ||| | | ||||| | || | || ||||| | | || || ||||||||| ||||||||||||||||| ||||||||||||||||| || | ||||||||||| || |||| |||||||||||||| |||||||| |||||||| |
tggttaattttaatgaattcatttgcgagcagatgaatgcttcatttccatttaatataagttctatcagggatgctaatctattttttattgtttgaagTGCTTATATGGAGGTGCTCCAAAAGGTCCTCAGCTAAGGGAGTTGGAGCGTGGTGCCGATGTTGTTGTTGCAACTCCTGGGAGATTGAACGACATTTTGG
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G462134_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------------gtacgttcctcctatcttttactcatctgttatgcgtttt---tgtgtcctataaagttgatgtcatctaattgtacctttttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG-------------
| | | | | | ||| | | | ||| | ||| ||| ||||| | || || | || || ||||||||| ||||||||||||||||| ||||| |||||||||||||| | ||||||||||| |||||||| || |||| |||||| ||||| ||||||||||| |
gtccaacagtattagttttgtctccaaccagggaattggcgacacaaattcaagatgaagcaatcaagtttgacaaatcttcatatgtgagcagttgaattcatatgtgagcagatgaacattccatttacatttaatatatgttatatgtcagggatgttaattatttttg--ttgttgtttgaagtgattatatggagGTGCTCCAAAAGGCCCTCAGCTAAGAGAGTTGGAGCGTGGTGCTGACATTGTTGTCGCAATTCCTGGGAGATTAAATGACATTTTGGAAATGAATAGAGT
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G481227_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------------gtacgttcctcctatcttttactcatctgttatgcgtttt---tgtgtcctataaagttgatgtcatctaattgtacctttttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG-------------
| | | | | | ||| | | | ||| | ||| ||| ||||| | || || | || || ||||||||| ||||||||||||||||| ||||| |||||||||||||| | ||||||||||| |||||||| || |||| |||||| ||||| ||||| ||||| |
gtccaaccgtattagttttgtctccaaccagggaattggcgacacaaattcaagatgaagcaatcaagtttgatagatcttcatatgtgagcagttgaattcatatgtgagcagatgaacattccatttacatttaatatatgttatatgtcagggatgttaattatttttg--ttgttgtttgaagtgattatatggagGTGCTCCAAAAGGCCCTCAGCTAAGAGAGTTGGAGCGTGGTGCTGACATTGTTGTCGCAATTCCTGGGAGATTAAATGATATTTTGGAAATGAATAGAGT
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G01540.3 (Arabidopsis thaliana), 3'ss of exon 5
----gtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatt--------tgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG
||| ||| | ||| || | |||| | ||||| |||| | | || | || ||| | ||||| | ||||||| ||||| ||||| || || || |||||| | || ||| |||| | || ||||| || ||||||||||||||||| ||||||||||| || | |
gtatgtagaagtctctgaacttgtaaagtttcaacatgc-tacttgtgaagtatatgtctaacgtatgccaaatgtgtggtcttattatctctgtttcagTGTTTGTATGGTGGTGCACCAAAGGGCCCTCAGTTGAGGGATTTAGAAAGAGGAGCAGATATCGTGGTTGCAACTCCTGGGAGATTGAATGATATCCTTG
upper sequence: LOC_Os01g07740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S35_3V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------------------gtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatt-----------tgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG
|| | | | ||| | || | | |||| | || ||| || | | || | | ||||||||| || ||||||||||||| |||||||| || ||||||||||| |||| | || ||||| | ||||||| | ||||| || ||| | ||||| ||| |||| |
gtgcgtcttctgtagatgatcagttttctccaacgaacagctgtcactgtcgatgaataacaccacaactcaaacggtcgatcatcgtgtgacaagcttgtctcagatcacgttgcgttaagacattgtattttagaaaa--aatctgagaaaacttcagctttttattcctcgtgtgaatgcagTGTTTATATGGTGGTGCTCCGAAGGGTCCTCAGCTCCGAGACATTGAACGTGGAGTGGACATTGCCATAGCAACCCCAGGACGCTTGAACGACTTTTTGGMapped 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|58594039|gb|CF992347.1|CF992347EST: TCCAAGATGAAGCAAAAAAGTTTGGGAGATCATCAAGAATATCGTCTGTT TGTCTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGC
genomic: TCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcct ... ttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGT
EST:
gi|2310452|gb|C26607.1|C26607EST: TCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTT TGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGT
genomic: TCCAAGATGAAGCGAAAAAGTTTGGGAGATCGTCAAGAATATCGTCTGTTgtacgttcct ... ttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG
atctaat putative branch site (score: 3)
cctttttattt putative PPT
tttttatttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttcctcctatcttttactcatctgttatgcgtttttgtgtcctataaagttgatgtcatctaattgtacctttttatttgaagTGTTTATATGGAGGTGCTCCTAAAGGTCCTCAGCTAAGAGATCTAGAGCGTGGTGCAGACATTGTGGTTGCAACTCCTGGAAGATTGAATGACATTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA