Sequence
atgc intronic sequence ATGC exonic sequence...caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g30840.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085670_T06 (Zea mays), 3'ss of exon 3
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | |||| ||||| || ||| ||| |||| ||| || ||||| | ||| |||| | ||||| | |||||||||||||| ||||||||||| ||||||||||||||
gaagcgttcttgtagcaaaatcttttactttcta-ttccatactatatttttcctgtag--aattctaa-tgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAAC---------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152805_T01 (Zea mays), 3'ss of exon 3
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | | || ||||| || ||| ||| |||| ||| || ||||| | ||| |||| | ||||| | |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||
gaagcgttcttgtagcaaaatcttttactttcta-ttccataccatatttttcctgtag--aattctaa-tgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G115277_T02 (Zea mays), 3'ss of exon 3
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attat-catttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | | || ||||| || ||| ||| |||| ||| || ||||| | ||| ||| | ||||| | |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||
gaagcgttcttgtagcaaaatcttttactttcta-ttccataccatatttttcctgtag--aattctaa-tgtactcctttttttactatatttttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152100_T01 (Zea mays), 3'ss of exon 3
-caagttcatgtagtattatcttttaccttaaaactctgt-tctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAG-AATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
||| | | | | | | | ||| | | | || | | | ||| ||| | || | |||| || | | ||| | || | | |||| ||| | |||| || ||
gtaagagaactcgaagattttctaatcaatgagtgcatgtatgcaagagttggatgtttccaacg-taagagaactcgaagattatgcatgttcatgta-gGGTATTGTCAGA-GGCAAACTGGATCAACTGAGAAGATGCTTTGAA----------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152100_T01 (Zea mays), 3'ss of exon 3
-caagttcatgtagtattatcttttaccttaaaactctgt-tctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAG-AATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
||| | | | | | | | ||| | | | || | | | ||| ||| | || | |||| || | | ||| | || | | |||| ||| | |||| || ||
gtaagagaactcgaagattttctaatcaatgagtgcatgtatgcaagagttggatgtttccaacg-taagagaactcgaagattatgcatgttcatgta-gGGTATTGTCAGA-GGCAAACTGGATCAACTGAGAAGATGCTTTGAA----------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G027551_T01 (Zea mays), 3'ss of exon 1
---caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | |||| |||| || | ||| |||| ||| || ||||| | ||| |||| | ||||| | |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| |
ataagcgttcttgtagcaaaatcttttactttcta-ttccatactatattttc---ctacagaattctaa-tgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152100_T02 (Zea mays), 3'ss of exon 2
caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
||| |||||| || | | ||| | | || | || | | | | |||| || | | |||||||| |||| |||| || ||
----------------------------------agagttggatgtttccaacgta-agagaactcgaagattatgcatgttcatgtagGGTATTGTCAGAGGCAA--ACTGGATCAACT-----GAGAA---GATGCTTTGAA----------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 3
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | |||| ||||| || ||| ||| |||| ||| || ||||| | ||| |||| | ||||| | |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||
gaagcgttcttgtagcaaaatcttttactttcta-ttccatactatatttttcctgtag--aattctaa-tgtactcctttttttactataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATTCA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152100_T01 (Zea mays), 3'ss of exon 2
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | |||| ||||| || ||| ||| |||| ||| || ||||| ||||| |||| | ||||| | |||||||||||||| ||||||||||| ||||||||||||||
gaagcgttcttgtagcaaaatcttttactttcta-ttccatactatatttttcctgtag--aattctaa-tgtactcctttttttattataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAAC---------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152100_T02 (Zea mays), 3'ss of exon 1
--caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggttttt-attatcatttcta-ttcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
|||| ||||| | ||||||||| || | || | |||| ||||| || ||| ||| |||| ||| || ||||| ||||| |||| | ||||| | |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||||||| |
gaagcgttcttgtagcaaaatcttttactttcta-ttccatactatatttttcctgtag--aattctaa-tgtactcctttttttattataattttttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTGGATGTTTCCAACGTAAGAGAACTCGAAGATTTTCTAATCAATGAGTGCATGTATGCA
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 2
----caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
| ||| | | | | | | |||| | | || || | || || | |||| || ||| || |||| ||||| | |||||||||||||| ||||||||||| || || ||||| |||||||||||||||||||||||||| ||||||||||||||||| |||
cgactatcttcccggcgccgtttatccccgttatgaactaggattcataacactg--tagaactctaaggtactcacttgtttactataattctttc--ttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGAGAACTCGAAGATTTCCTAATCAATGAGTGCATGTATTCG
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G027551_T01 (Zea mays), 3'ss of exon 2
caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
||| |||||| || | | || | | | || || | | | |||| || | | ||||| || |||| |||| || ||
----------------------------------agagttggatgtttccaacgtaagagaacttgaagattatgcatgttcat-gtagGGTATTGTCAGAGGCAA--ACTAGATCAGCT-----GAGAA---GATGCTTTGAA----------------------------------------------
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 4
---------------------caagttcatgta-gtat-tatcttttaccttaaaac-tctgttctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAAC-TCATG-CAAGAATTGGATGTTT-CCAATGTAAGAGAAC--TCGAAGATTTCCTCATCAA-TGAGTGCATGTACTCG-
| | | ||| | || ||| | || || || | || |||| ||| | | || | | | | || || ||| | ||||| | | ||| ||| | || |||| | | ||| || | ||| | | | | | || | | |||| |||| || |
gtaagagaactcgaagatttcctaatcaatgagtgcatgtattcggtgagttgttacatcctctttaaattttggctctgg--tatttttcttattttcagtggtttttaatacttctagtgttgc-ctaaagtatttttgacatcatatccataatattctgcatgttcatgcagGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 3
caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttt-tattatca--tttctatt-------cagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
| | | || | |||| | || || | | || || || |||| | ||| ||| || |||| ||| | | ||| | || ||||| || || ||||||||||| ||||| ||||| |||||| | |||||| | ||||| |||||||| || ||||||||||||||||| ||
--------tccattttttttttttccattttgcttcca--ccaaattcctgattatgacagttgcaaacttgcatgattttctatgactaattttttgttacttgcccagGTACTCCCCTATGATCAACTGATGCAGGAATTAGATGTTACAAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATGTATGCG
upper sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0234g00120.t01 (Vitis vinifera), 3'ss of exon 3
caagttcatgtagtattatcttttaccttaaaact-ctgttctatgtttttgctttagacaatactaaat-gtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
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--tggttatgaaggagttccctttctgttgatatcattaataggattttttgtaacgcataaacttgtattgaactttcttattaatgtttgaattttccagGTTCTCTCCTACTATCAACTGATGCAGGAACTTGATATTTCTAATGTACGTGAACTTGAAGATTTTCTTATCAATGAGTGCATCAATGCGMapped 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|88363229|gb|CI643087.1|CI643087EST: TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAG GTGCTACCATATGATCAACTCATGCAAG
genomic: TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaattt ... ttctattcagGTGCTACCATATGATCAACTCATGCAAG
EST:
gi|86821685|gb|CI309190.1|CI309190EST: TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAG GTGCTGCCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGA
genomic: TCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaattt ... ttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
tactaaa putative branch site (score: 1)
tttctattc putative PPT
tttttattatcatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagttcatgtagtattatcttttaccttaaaactctgttctatgtttttgctttagacaatactaaatgtgcttggtttttattatcatttctattcagGTGCTACCATATGATCAACTCATGCAAGAATTGGATGTTTCCAATGTAAGAGAACTCGAAGATTTCCTCATCAATGAGTGCATGTACTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA