Sequence
atgc intronic sequence ATGC exonic sequence...taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g57140.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 20
-taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattt-tccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
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atatttctgctggaactaa-agtccttgagctgt-tgcaattaatgtccaagtttgtttcatattaaagggaagaattgacagtgtttctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCAGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAAGTATAAATAAATCTCTTTCTG
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
----taattaattaagaataaataaactctgcacaga-acacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
|| || | | |||| | | || | | | | | | | | || || | | | | ||| | || || ||||||||||||||| |||||||||||||||||||||||||||||||| || || || |||||||| |||||||||||||| ||||| || || || ||||||||||
tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgacagtgt-----tcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G109420_T01 (Zea mays), 3'ss of exon 6
taattaattaagaataaataaactctgcacagaa---cacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattt-tccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
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gtacgcgttgcgcgccactgcacgccgaggcgaagctttcgccgatggcgatgactagctggcctatctacgtacgaattgacagTGTTTCTCTGTTTGAACAGCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAG---------------------
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G109420_T01 (Zea mays), 3'ss of exon 7
taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGG-TGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG-------------------------------------------------------
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--------------------------------------------------tcatattaaagggaagaattgacag-tgt-----ttctctgtttgaatagctaagttttgtggaccttggtggttctgagaggggtgaaaaaatctggttccgcagGAAAGCAATTGAAAGAAGCGCAAAGTATAAATAAATCTCTTTCTGCTTTGGCTGATGTTATTGGTTCTTTATCTTCTGATGGACAACATATACCTTACCG
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 25
---------taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
|| || | | || ||| || | | | | | | || |||| | ||| | |||| || | | | ||| | || ||||||||||| ||||| ||||||||||| || || ||||||||||| || || | || | || || || |||||||| ||||| || ||||| | || |
cagggaaaaatgtttcttcattgttaagcaacaatgtggaacattgattgtttcttgagctcg-tggtgcgtgcttatttta---tcttgga---ttcaatatg--cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACCGGGAGTCAGCTTAAGGAAGCTCAGAGCATTAACAAGTCATTATCAG
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 22
--------------------------------------------------------------taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctatt--ctaagctgt-caaaattttccgtgtga---acagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
| || || | | || | ||| || | | |||| | |||| || | | || || | | | |||| | | || |||| ||||||| ||||| |||||||| || || || || |||||||| ||||| |||| | ||||| |||||||||||||| ||||| || || | || |
gtattggtgtacattacttcaattttacctttgaatatcagtatgaatgttaatataccatattcttcctttattttgtggcaatttgaaacacaa-gtattttatgacct-cgaggcattgcagtttttttaacttttttatgctggatttgtcatttgtcatacagTTAAGTTTTGTGGATCTTGCTGGCTCAGAAAGAGTAAAAAAGTCGGGCTCTTCAGGTAGTCAACTTAAAGAAGCTCAAAGTATCAACAAATCATTATCAG
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
---taattaattaagaataaataaact-ctgcacagaacacactatatg-ttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
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atattattagtcaatgatatgccctccattgttaaacccatatcacctgatcatggtggtatcttctacaatattctgaatttttg---tttgttatttg--cagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
upper sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
-----taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
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aatctgtgttaacatggagtgtgagatgtcttgttggggcttact-tattgtgataatgtttatttgtctttacatgacaattttaaaactctatctg----cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAGMapped 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|218496230|gb|FG959153.1|FG959153EST: TCATTATAGAAAGTACCAACCTCCAGACTCAATCTTATGCACGAGGAAAG CTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCA
genomic: TCATTATTGAAAGTACCAACCTCCAGACTCAATCTTATGCAAGAGGAAAGgtatggtggg ... gtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
ttttccgt CT-rich tract
tcaaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattaattaagaataaataaactctgcacagaacacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - -gaataaa
- - - - - - - - - - - ctctgca
- - - - - - - - - - - - - - - -gaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtca