Sequence
atgc intronic sequence ATGC exonic sequence...atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g65330.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 5
atatactgttaactg-catcttactatcaatctgctggcatttatcagttttcttctttt--gcatgtcttgtt---gaaattacaaatt---tcaatttttt---tttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
||| ||| ||| | || ||| ||||||| ||||||| | ||||||| || | |||| | || ||| ||| | ||| ||| | ||| ||||||||||||||||||||||||| |||||||||||| |||||||||||||||| |||||||| |||||||||||||| ||||| |||||||
--------ttagctgtcattctcctg--gatc--ctggcatctatcagtcctgttcttttcagcctttcttttctccaaatttataaactctgtcatctttctaacttttagGAACTATACCATGAAATGCATGCCCTGGATAGATTTCAACAAGATTATCAGCGTAAACAGCATGAAGAGGATGGTTCTAGTGTTGTGCAAAGAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 4
atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgtt-------gaaattacaaatt---tcaatttttt---tttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
|| | || ||| ||| ||||||| || |||| | ||||||| | | || | || ||| ||| | ||| ||| | ||| ||||||||||||||||||||||||| |||||||||||| |||||||||||||||| |||||||| ||||| |||||||||||||| |||||||
-------------caaatttagctttcattctcctggcatataccagtactgttcttttcattttttttcttttctccaaatttataaactgtatcatctttctaacttttagGAACTATACCATGAAATGCATGCCCTGGATAGATTTCAACAAGATTATCAGCGTAAACAGCATGAAGAAGATGGTTCAAGTGTTGTGCAAAGAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
------atatac-tgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
|| || | | | | | || | || | | || | ||| | || || | ||||| || ||| | | | | | |||||| |||| |||||| ||||||| | ||||||||||| |||||||||| |||||| || |||||||| ||||| || |||||||
gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgtt---aagtctt----aatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 4
atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttt--tttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
||| | | || | | | | | | | || || | | |||||| |||||| ||| | | |||| | ||||||| |||||||||| ||||||| |||||||||||| |||||||||||||| || | | || || ||| |||| ||| | ||||| |
--gccctgcttttttaattcattcaactttgcctttatttcttttggtgttggtgggatttatgtctgaaagaaattggaaaatcgatttttatggcctcagGAATTATACCATGAGTTGCATGCTTTGGATAGATTTGCACAAGATTATCAGCATAAGCGTGAAGAGGATGATAATTCAGGTGCAGCTCAAAGTG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G33040.1 (Glycine max), 3'ss of exon 4
---atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttt--tttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
| | | |||| | ||| ||| || | | | | | | || || | | | |||| |||||| ||| | | |||| | ||||||| |||||||||| | ||||| |||||||||||| |||||||||||||| || | | || || ||| |||| ||| | ||||| |
gccctgcatttttaatt-cattcaactgtctttttatt----tctttttgtgtttgtgggatttaagtctgaaagaaattggaaaatcaatttttatggcctcagGAATTATACCATGAGTTACATGCTTTGGATAGATTTGCACAAGATTATCAGCATAAGCGTGAAGAGGATGATAATTCAGGTGCAGCTCAAAGTG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 3
atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttt----tttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
| || | ||||| | | | || || | | || |||| | | | | | ||| | | |||||||| | | |||||| | ||||||||| | ||||| |||||||||||||||||||| ||||||||| |||| ||||| | | ||| |
---aagtgctccatgcatttgcttttttattcaatg-tagtaattttttttatgtgggggtttatttctgaaaaaattggacaatcaattttctgtgactgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGATCAAAGAG------------
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 4
atatactgttaactgcatcttactatcaatctgctggcatt-tatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaattttttt---ttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
|| || ||| | | | | | | || | ||| | |||| || | | | | | | ||||| ||| | | ||| | | | |||||| | ||||||||| | ||||| |||||||||||||||||||| ||||||||| |||| ||||| || | |||||||
----acgaccaagtgctccatgcatttgctttttattcaatgtataaatttttttatgtgggggtttatttctaaattggaaaatcaattttctgtggctgcagGAATTGTACCATGAATTACATGCTTTGGATAGATTTGAACAAGATATTCAGCGCAAGGGTGAGGAGGAGGAGGG---------GGATCAAAGAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 7
-atatactgttaactgcatcttactatcaatctgctggc-atttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
| | | | | | | | | | | | || | | | | ||| || | | | || | || | ||| ||| | |||||| ||||||||||| ||||||| | || |||||||| |||||||||| |||||| | || |||||||| ||||| || |||||||
tagacatcctgatggaaagttggttcttatttctttagctgtacagctgattttatcaagacctgatttcatttagtttg--acttttttctttgcgtgcagGAATTATACCATGAATTGCATGCCTTAGACAGATTTGATCAAGATTATCGGCGCAAGCTTCAAGAAGAGGACAATTCAAATGCTACACAAAGAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
atatac-tgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaattttttttt-cagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
||| || | | ||| | | | | ||| || | | | |||| || || | || ||| | | || |||| || |||||| |||| ||||| ||||||| |||| ||||||||||||||||||| |||||| | |||||||||||| || | || | ||| |||
gtatttgtgatgatgacatgatcttgtaa--ttgcaagcttatgcaaatttttacgcttaaacagttagcagggaaagacataatgcatcttttggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAGMapped 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|29680203|gb|CB676478.1|CB676478EST: AGGCAGAATCAGTGATGCAACAATTGGTGACTTGTGTTCAGTGCACAGCT GAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAG
genomic: AGGCAGAATCAGTGATGCAACAATTGGTGACTTGTGTTCAGTGCACAGCTgtaagtaatg ... tttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAG
EST:
gi|33799472|gb|CF325594.1|CF325594EST: AGGCAGAATCAGTGATGCAACAATTGGTGACTTGTGTTCAGTGCACAGCT GAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAG
genomic: AGGCAGAATCAGTGATGCAACAATTGGTGACTTGTGTTCAGTGCACAGCTgtaagtaatg ... tttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
tttcaatttttttttc CT-rich tract
ttgttgaaattacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatactgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG