Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 10
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatc-cagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
||||||||||||| |||| |||| | || | |||||||||| | ||| | |||| | | || |||| | || || | | | | |||| ||| |||||||||||||| |||||||||| |||||||||||||| ||||||||| |||||||||||||||||||||| || ||||||||||| | |||||| |
gtaatttcttaatgttctcatcttcttctttc--tgaaaagtgtcgtgtcattataaaaaaaactgcatgctattat-cttattctttttgtctgtatg-----------cagATTAATCCAAAAGCTACAGAGTCTCTAGCAGATCCTTCTGAATATCCAAATCTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGTGTTGCGT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 20
gtaatttcttaatcttctgctctta-tctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
||||||||||||| |||| ||||| |||| ||||||||||| | |||| |||||| | | || |||| | | | || || | ||| |||| | | ||| |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||| | |||||||
gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccatt-agaaaaaaatgcatgctattatcttattctt-----tttttctgtaccttgtatgcagATTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAATATCCAAATTTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGCGTTGCTT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 21
gtaatttcttaatcttctgctctta-tctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
||||||||||||| |||| ||||| |||| |||||||||| | ||| |||| | | || |||| | || || | | | | |||| ||| ||||||||||||||||||||||||| |||||||||||||| ||||||||| |||||||||||||||||||||| || ||||||||||| | |||||| |
gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtcgtgtcattagaaaaaaactgcatgctattat-cttattctttttgtctgtatg-----------cagATTAATCCAAAAGCTGCAGAGTCTCTAGCAGATCCTTCTGAATATCCAAATCTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGTGTTGCGT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 6
gtaatttcttaatcttctgctctta-tctttgcattgaaaagtgtgcttccatc-cagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
||||||||||||| |||| ||||| |||| |||||||||| | ||| | |||| | | || |||| | || || | | | | |||| ||| ||||||||||||||||||||||||| |||||||||||||| ||||||||| |||||||||||||||||||||| || ||||||||||| | |||||| |
gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtcatgtcattataaaaaaaactgcatgctattat-cttattctttttgtctgtatg-----------cagATTAATCCAAAAGCTGCAGAGTCTCTAGCAGATCCTTCTGAATATCCAAATCTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGTGTTGCGT
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
----------------------------------------------------------------------------gtaattt---cttaatcttctgctcttatct--ttgcattgaaaagtgt--gcttccatccagaaaacattttctgt------tattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
|| | | | |||||| ||| || ||| || || | ||| || |||| || | || | | || | |||| || |||| | || |||||||||||||||||| || || || |||| |||||| |||||||| ||||| ||||| || ||||| ||||||||| |||| ||| || | | |
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaata-tgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
|| | || || || | || || | | | | |||| ||| | | | | || | | |||| | |||| | || ||||||||||||||||||||| || || |||| |||||| || ||||| ||||| ||||| || ||||| |||||||| |||| ||| || | | |
-------ctcattccattggcctg--ccctgtcctggattct-tatcatgctacagattgcatgtgaaataaaaatataaattct-tatatttagttgttaata-tgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
-gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
||| | | | | || | | | |||| ||| | | ||| || | || | ||| || | | || | || | | |||||||||||||||||||| || || |||| |||||| || ||||||||||| |||||||| |||||||||||||| |||| ||| || | ||
ggtaggagcatcagttctcattcatttgccttgtttgagtagtct--tatcatgttgacga--------gtggct--catggattaaagagagtacatatattttat-tgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
| | | | | | | |||| | | || | | | || | | || | | || |||| ||| | | | | | |||||||||||||||||||| || ||| |||| |||||| |||||||| ||||||||||| |||||||| |||| ||| | | ||| || |||||
--atatgcctgcttgggtagttggatctatttcatttaacttttcttgtgatttaaagaaagagacacatatctaatcctgtttgatcaacac----------tatatgcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCG
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
|| || ||| || | | | | | || | | || || ||||| | | || | || || ||| || | | | ||||| | |||||||||||| || ||||||||||| ||||| || ||||| ||||| |||||||||||||| ||| | ||| || || |
--catgtcataaa----tgaaccaagaaaagagataaggagaaagg---aaaggagtgaaaattttgaaccct--tcttgactgcata-atgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAGMapped 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|58658342|gb|CK047022.1|CK047022EST: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA GTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
genomic: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttctt ... ttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
EST:
gi|58665864|gb|CK054550.1|CK054550EST: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA GTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
genomic: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttctt ... ttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
EST:
gi|33679448|gb|CF307687.1|CF307687EST: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA GTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
genomic: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttctt ... ttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
EST:
gi|2310301|gb|C26456.1|C26456EST: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA GTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
genomic: CCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttctt ... ttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAAT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
73 (upstream exon),
70 (downstream exon)
Score:
15CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttctt ... ttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
tgttccttct CT-rich tract
ttttatctattcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA