Sequence
atgc intronic sequence ATGC exonic sequence...ttggatgcaacagaatgtgtaatgagatactaaataatcagagctagtgattctatgtttacatgacatatattctcattgctcaaattgctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCGTTCAATATTTCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50170.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G406177_T01 (Zea mays), 3'ss of exon 6
-------ttggatgcaacagaatgtgtaatgag--atactaaataatcagagctagtgattctatgtttacatgacatatattctcattgctcaaattgctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCGTTCAATATTTCTCAG
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aaaacatactattgccaccctgtttctgctgttccaaactgagatactaaggtt-gtgttgacaatcctacatgacatatatacttatt-ttcaa-------tttgcagATACAATATCCAAAATTTGGTCGATCACTTTCATGAGCGTGGTCTTTATCGTTCAATATTTCTCAG
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G437845_T01 (Zea mays), 3'ss of exon 7
-------ttggatgcaaca--gaatgtgtaatgagatactaaataatcagagctagtgattctatgtttacatgacatatattctcattgctcaaattgctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCGTTCAATATTTCTCAG
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aaaacatactattgccaccctgtttctgctcttccaaactgagatactaaggtt-gtgttgccaatcctacatgacatatatacttatt--ttaaa------tttgtagATACAATATCCAAAATTTGGTCGATCACTTTCATCAGTGTGGTCTTTATTGTTCAATATTTCTCAG
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G325504_T01 (Zea mays), 3'ss of exon 3
-------ttggatgcaaca--gaatgtgtaatgagatactaaataatcagagctagtgattctatgtttacatgacatatattctcattgctcaaattgctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGT--CTTTACCGTTCAATATTTCTCAG
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aaaacatactattgccaccctgattatgctgttccaaactgagatactaaggtt-gtgttgccaatcctacatgacatatatacttatt-ttcaa-------tttgcagATACAATATCCAAAATTTGGTCGATCACTTTCATGAGCGTGGTGTCTTTATAGTTCAATATTTCTCAGMapped 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|66926863|gb|CX113711.1|CX113711EST: ATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGG ATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCG
genomic: ATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggatagc ... ctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgattctatgtttacatgacatatattctcattgctcaaattgctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCGTTCAATATTTCTCAG
acatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggatgcaacagaatgtgtaatgagatactaaataatcagagctagtgattctatgtttacatgacatatattctcattgctcaaattgctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCGTTCAATATTTCTCAG
-tggatgc
- - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - -tgattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttacatg