Sequence
atgc intronic sequence ATGC exonic sequence...atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g21660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 5
-atctttgagctcctctgaaaa-gtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
| ||| | || || || | ||| ||| | ||| | |||| | || ||| ||| || | | |||||||| | | | |||| | | |||||||| ||||| | |||||| | ||||| |||||||||||||| ||||||||||| ||||| || || ||||||||||||||||| ||||
ttttcctgaaatactgcgaggtcaattttcagttcta--ttattgattatcttttcttagtttaatttagacgaacattaacatctttgtgaattgtttcagATGTTCATTGGTGATGGAGCTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
--atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtac--gattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
|| | | || || | | || | || || ||| || | | | || | || ||||| | | ||| | || |||| | | ||||| || ||||||| |||||||||||| |||||||| || || ||||| || | |||||||||||||| || |||||||||||||||||||
gtttcctctatttcacttgcaca----ctaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 5
atctttgagctcctctgaaaagttt-cttagtgctacatgatttgcctttttttttatgtac-gattgagatta----atactggtttc-tttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
|||||| || | | | |||| | ||||| | | || | | || || | || ||| || | | || | || |||| | | || || || ||||||| ||||||||||||||||||||| || || |||||||| | |||||||||||||| || |||||||||||||||||||
-------gtttcctctatttcacttgcacactactaccttatttgtttgtattcacgtctcttgactgggtttggattataatgatctaacctgcaattttgtacagATGTTCATAGGAGATGGAGCAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 3
----atctttgagctcctctgaaaagtttctta--gtgctacatgatttgcctttttttttatgtacgattgag--attaatac-tggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
|||||| || || | || |||||| | | |||| || || | | | | | || ||| || | | |||| | | | || | | | ||||| |||||| || |||||||||||||| || |||||||| | ||||||||||| || || ||||||||||||||
atcaatcttt---ttcagctaataattttcttgtgatttttgttgatgaaactcattgactgtatggggattagttattcttatattatgtcttcatat-taagGATATAAATATGCTTTGGTTCTAGCAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGC-----
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 5
atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
|||| | | | | | | | | ||| | | | | | || | ||| || | | || | | | |||| | |||| || || ||||||| |||||| | |||||||||||||| || |||||||| | ||||||||||| || || |||||||||||||||||||
atctatactattgttctacttgcgttagatgtttgcatacatgtctatgtgctgcatcagcatttggaatggaggaataatctaacctgaaattttacagATGTTTATAGGAGACGGAGCAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------------------------atctttgagctcctctgaaaa--gtttcttagtgct------acatgatttgcct--------ttttttttatgtacgattgagatta-atactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
| || | | |||| | | | |||||| | ||| | || | | | | | || ||||| || | || || | | | |||| | | ||||| || ||||||| ||||| |||||||||||||| ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| ||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatcca-atttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
-atctttgagctcctctgaa--aagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
|| | || | | || | || | | |||||| | || |||| | | | | ||| | ||| | ||| | | | |||| | | ||||| || || || | |||||| |||||||||||||||||||||||||||||| | || ||||| ||||| || |||||||||||||| || |
aattctctagttgccatgtagcaattatgttagtgtgatgtgtgcattctttgatctattcttttattaaatgtaa--ccaaacaacttg-gaatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 6
atctttgagctcctctgaaaagtttcttagtg-ctacatgatttgcctttttttt---tatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
||| | || ||| || | | || | | || ||| | ||| | | | | ||| | | || | | | |||| | | | |||| | | || || || || |||| ||||||||| ||||| || |||||||| ||||||||| ||||||| || ||||||||||||||||||||||| ||||
---attggttccaattgtaaaagttgtgactgtccatgagaattgttactatttgccatttatccatatgacaacattaattatctgcttgta-atgcatccagATGTTCATAGGGGATGGTGCAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgt-gcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
| | || | | | ||| ||| | || | || | | |||| | |||| ||||| | | || || || ||||||| || || | |||||||||||||| || |||||||| || || ||||| |||||||| |||||| | || || ||||
-------------------------------gttctgtg--taggaactctttacctgtcgggttc--ttaaactcaagcttct-----ggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG
upper sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
| | || | | | ||| ||| | ||| |||| | |||| | ||||| | | || || || ||||||| || || | |||||||||||||| || |||||||| || || ||||| |||||||| |||||| | || || ||||
-------------------------------gttctgtg--taggaactctttacctgtcgggttg---ttaaactcaagcttcttgttcgtt---gcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTGMapped 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|33381485|gb|CF196828.1|CF196828EST: CCCAGACAAATGCAACATTTCTTAAGCTAACTGGTCCACAACTTGCCGTG AAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCT
genomic: CCCAGACAAATGCAACATTTCTTAAGCTAACTGGTCCACAACTTGCCGTGgtaattatct ... actcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
gattaat putative branch site (score: 3)
tttttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtacgattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - -agctcct
- - - - - - - - - - - - - - -gtgctac